Batch Script

@MARK22789939tokh 

This version uses a simple prompt input to enter in the opacity value rather than using a fixed 50% value:

/*
Combine and Average Images via Prompt from 2 Input Folders to Output Folder.jsx
https://community.adobe.com/t5/photoshop-ecosystem-discussions/batch-script/td-p/12700356
Stephen Marsh, v1.0 - 23rd January 2021
*/

#target photoshop

(function () {

    if (app.documents.length === 0) {

        try {

            // Input folder 1
            var folder1 = Folder.selectDialog("Select the first folder:");
            if (folder1 === null) {
                alert('Script cancelled!');
                return;
            }

            // Input folder 2
            var folder2 = Folder.selectDialog("Select the second folder to layer:");
            if (folder2 === null) {
                alert('Script cancelled!');
                return;
            }

            // Validate input folder selection
            var validateInputDir = (folder1.fsName === folder2.fsName);
            if (validateInputDir === true) {
                alert("Script cancelled as both the input folders are the same!");
                return;
            }

            // Limit the file input to jpg/jpeg
            var list1 = folder1.getFiles(/\.(jpg|jpeg)$/i);
            var list2 = folder2.getFiles(/\.(jpg|jpeg)$/i);

            // Alpha-numeric sort
            list1.sort();
            list2.sort();

            // Validate that folder 1 & 2 lists are not empty 
            var validateEmptyList = (list1.length > 0 && list2.length > 0);
            if (validateEmptyList === false) {
                alert("Script cancelled as one of the input folders is empty!");
                return;
            }

            // Validate that the item count in folder 1 & 2 matches
            var validateListLength = (list1.length === list2.length);
            if (validateListLength === false) {
                alert("Script cancelled as the input folders don't have equal quantities of images!");
                return;
            }

            // Output folder
            var saveFolder = Folder.selectDialog("Please select the folder to save to...");

            // Prompt input for layer opacity variable
            // Loop the input prompt until a number is entered
            var lyrOpacity;
            while (isNaN(lyrOpacity = prompt("Layer opacity % value:", "50")));
            // Test if cancel returns null, then terminate the script
            if (lyrOpacity === null) {
                alert('Script cancelled!');
                return
            }
            /*
            // Test if an empty string is returned, then terminate the script 
            if (lyrOpacity === "") {
                alert('A value was not entered, script cancelled!');
                return
            }
            */
            // Test if an empty string is returned, then repeat 
            while (lyrOpacity.length === 0) {
                lyrOpacity = prompt("Blank value not accepted, please enter the layer opacity % value:", "");
            }
            // Convert decimal input to integer
            var lyrOpacityInteger = parseInt(lyrOpacity);

            // Save and set the dialog display settings
            var savedDisplayDialogs = app.displayDialogs;
            app.displayDialogs = DialogModes.NO;

            // JPEG save options
            var jpgOptions = new JPEGSaveOptions();
            jpgOptions.formatOptions = FormatOptions.STANDARDBASELINE;
            jpgOptions.embedColorProfile = true;
            jpgOptions.matte = MatteType.NONE;
            jpgOptions.quality = 12;

            // Perform the stacking and saving
            for (var i = 0; i < list1.length; i++) {
                var doc = open(list1[i]);
                var docName = doc.name.replace(/(?:^.+_\d+_)(.+)(?:\.[^\.]+$)/, 'proc_$1');
                placeFile(list2[i], 100);
                // Change the upper layer opacity to variable from prompt
                doc.activeLayer.opacity = lyrOpacityInteger;
                doc.saveAs(new File(saveFolder + '/' + docName + '.jpg'), jpgOptions);
                doc.close(SaveOptions.DONOTSAVECHANGES);
            }

            // End of script
            app.displayDialogs = savedDisplayDialogs;
            app.beep();
            var listCount = list1.length;
            alert('Script completed!' + '\r' + listCount + ' JPEG files saved to:' + '\r' + saveFolder.fsName);

        } catch (err) {
            while (app.documents.length > 0) {
                app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
            }
            alert("An unexpected error has occurred!");
        }

    } else {
        alert('Please close all open documents before running this script!');
    }

    function placeFile(file, scale) {
        try {
            var idPlc = charIDToTypeID("Plc ");
            var desc2 = new ActionDescriptor();
            var idnull = charIDToTypeID("null");
            desc2.putPath(idnull, new File(file));
            var idFTcs = charIDToTypeID("FTcs");
            var idQCSt = charIDToTypeID("QCSt");
            var idQcsa = charIDToTypeID("Qcsa");
            desc2.putEnumerated(idFTcs, idQCSt, idQcsa);
            var idOfst = charIDToTypeID("Ofst");
            var desc3 = new ActionDescriptor();
            var idHrzn = charIDToTypeID("Hrzn");
            var idPxl = charIDToTypeID("#Pxl");
            desc3.putUnitDouble(idHrzn, idPxl, 0.000000);
            var idVrtc = charIDToTypeID("Vrtc");
            var idPxl = charIDToTypeID("#Pxl");
            desc3.putUnitDouble(idVrtc, idPxl, 0.000000);
            var idOfst = charIDToTypeID("Ofst");
            desc2.putObject(idOfst, idOfst, desc3);
            var idWdth = charIDToTypeID("Wdth");
            var idPrc = charIDToTypeID("#Prc");
            desc2.putUnitDouble(idWdth, idPrc, scale);
            var idHght = charIDToTypeID("Hght");
            var idPrc = charIDToTypeID("#Prc");
            desc2.putUnitDouble(idHght, idPrc, scale);
            var idAntA = charIDToTypeID("AntA");
            desc2.putBoolean(idAntA, true);
            executeAction(idPlc, desc2, DialogModes.NO);
        } catch (e) {}
    }

}());

https://prepression.blogspot.com/2017/11/downloading-and-installing-adobe-scripts.html

EDIT: Updated code from a private message request, adding a user prompt for a levels midtone/gamma value:

/*
Combine and Average Images via Prompt from 2 Input Folders to Output Folder v1-1.jsx
https://community.adobe.com/t5/photoshop-ecosystem-discussions/batch-script/td-p/12700356
Stephen Marsh, v1.1 - 21st October 2022
*/

#target photoshop

    (function () {

        if (app.documents.length === 0) {

            try {

                // Input folder 1
                var folder1 = Folder.selectDialog("Select the first folder:");
                if (folder1 === null) {
                    alert('Script cancelled!');
                    return;
                }

                // Input folder 2
                var folder2 = Folder.selectDialog("Select the second folder to layer:");
                if (folder2 === null) {
                    alert('Script cancelled!');
                    return;
                }

                // Validate input folder selection
                var validateInputDir = (folder1.fsName === folder2.fsName);
                if (validateInputDir === true) {
                    alert("Script cancelled as both the input folders are the same!");
                    return;
                }

                // Limit the file input to jpg/jpeg
                var list1 = folder1.getFiles(/\.(jpg|jpeg)$/i);
                var list2 = folder2.getFiles(/\.(jpg|jpeg)$/i);

                // Alpha-numeric sort
                list1.sort();
                list2.sort();

                // Validate that folder 1 & 2 lists are not empty 
                var validateEmptyList = (list1.length > 0 && list2.length > 0);
                if (validateEmptyList === false) {
                    alert("Script cancelled as one of the input folders is empty!");
                    return;
                }

                // Validate that the item count in folder 1 & 2 matches
                var validateListLength = (list1.length === list2.length);
                if (validateListLength === false) {
                    alert("Script cancelled as the input folders don't have equal quantities of images!");
                    return;
                }

                // Output folder
                var saveFolder = Folder.selectDialog("Please select the folder to save to...");

                // Prompt input for layer opacity variable
                // Loop the input prompt until a number is entered
                var lyrOpacity;
                while (isNaN(lyrOpacity = prompt("Layer opacity % value:", "50")));
                // Test if cancel returns null, then terminate the script
                if (lyrOpacity === null) {
                    alert('Script cancelled!');
                    return
                }
                /*
                // Test if an empty string is returned, then terminate the script 
                if (lyrOpacity === "") {
                    alert('A value was not entered, script cancelled!');
                    return
                }
                */
                // Test if an empty string is returned, then repeat 
                while (lyrOpacity.length === 0) {
                    lyrOpacity = prompt("Blank value not accepted, please enter the layer opacity % value:", "");
                }
                // Convert decimal input to integer
                var lyrOpacityInteger = parseInt(lyrOpacity);

                // Prompt input for levels gamma variable
                // Loop the input prompt until a number is entered
                var gammaValue;
                while (isNaN(gammaValue = prompt("Levels Gamma (9.99 - 0.01):", "1.00")));
                // Test if cancel returns null, then terminate the script
                if (gammaValue === null) {
                    alert('Script cancelled!');
                    return
                }
                // Test if an empty string is returned, then repeat 
                while (gammaValue.length === 0) {
                    gammaValue = prompt("Blank value not accepted, please enter the layer opacity % value:", "");
                }

                // Save and set the dialog display settings
                var savedDisplayDialogs = app.displayDialogs;
                app.displayDialogs = DialogModes.NO;

                // JPEG save options
                var jpgOptions = new JPEGSaveOptions();
                jpgOptions.formatOptions = FormatOptions.STANDARDBASELINE;
                jpgOptions.embedColorProfile = true;
                jpgOptions.matte = MatteType.NONE;
                jpgOptions.quality = 12;

                // Perform the stacking and saving
                for (var i = 0; i < list1.length; i++) {
                    var doc = open(list1[i]);
                    var docName = doc.name.replace(/(?:^.+_\d+_)(.+)(?:\.[^\.]+$)/, 'proc_$1');
                    placeFile(list2[i], 100);
                    // Change the upper layer opacity to variable from prompt
                    doc.activeLayer.opacity = lyrOpacityInteger;
                    app.runMenuItem(stringIDToTypeID('rasterizePlaced'));
                    try {
                        doc.activeLayer.adjustLevels(0, 255, gammaValue, 0, 255);
                    } catch (e) {}
                    doc.saveAs(new File(saveFolder + '/' + docName), jpgOptions);
                    doc.close(SaveOptions.DONOTSAVECHANGES);
                }

                // End of script
                app.displayDialogs = savedDisplayDialogs;
                app.beep();
                var listCount = list1.length;
                alert('Script completed!' + '\r' + listCount + ' JPEG files saved to:' + '\r' + saveFolder.fsName);

            } catch (err) {
                while (app.documents.length > 0) {
                    app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
                }
                alert("An unexpected error has occurred!");
            }

        } else {
            alert('Please close all open documents before running this script!');
        }

        function placeFile(file, scale) {
            try {
                var idPlc = charIDToTypeID("Plc ");
                var desc2 = new ActionDescriptor();
                var idnull = charIDToTypeID("null");
                desc2.putPath(idnull, new File(file));
                var idFTcs = charIDToTypeID("FTcs");
                var idQCSt = charIDToTypeID("QCSt");
                var idQcsa = charIDToTypeID("Qcsa");
                desc2.putEnumerated(idFTcs, idQCSt, idQcsa);
                var idOfst = charIDToTypeID("Ofst");
                var desc3 = new ActionDescriptor();
                var idHrzn = charIDToTypeID("Hrzn");
                var idPxl = charIDToTypeID("#Pxl");
                desc3.putUnitDouble(idHrzn, idPxl, 0.000000);
                var idVrtc = charIDToTypeID("Vrtc");
                var idPxl = charIDToTypeID("#Pxl");
                desc3.putUnitDouble(idVrtc, idPxl, 0.000000);
                var idOfst = charIDToTypeID("Ofst");
                desc2.putObject(idOfst, idOfst, desc3);
                var idWdth = charIDToTypeID("Wdth");
                var idPrc = charIDToTypeID("#Prc");
                desc2.putUnitDouble(idWdth, idPrc, scale);
                var idHght = charIDToTypeID("Hght");
                var idPrc = charIDToTypeID("#Prc");
                desc2.putUnitDouble(idHght, idPrc, scale);
                var idAntA = charIDToTypeID("AntA");
                desc2.putBoolean(idAntA, true);
                executeAction(idPlc, desc2, DialogModes.NO);
            } catch (e) {}
        }
    }());

As a start, you can find existing scripts to do most of what you want: