How to I batch automate combining files as layers

OK, this is far from perfect, however, it is the best that I can currently do (I still consider myself a beginner).

You should temporarily move the files that don't have a matching _a.bmp alpha file to a temporary folder so that they are not processed.

Hope this helps.

WARNINGS & NOTES FOR USE:

•  Use at your own risk!!!
•  There must be multiple pairs of files, not an odd number of input files, there is no error checking
•  Work on copies of the original files until you are happy with the results
•  The original .bmp file will be overwritten, I did I mention to use at your own risk and to work on copies!
•  The code could be adjusted to save the adjusted file with a new name rather than overwrite the original (there are 10,000+ files to consider)
•  The alpha _a.bmp files will be closed without saving changes
•  Only the top-level folder will be processed, sub-directories must be processed separately
•  A selection will be loaded from the RGB composite channel of the alpha data
•  An action will then be run to complete the processing using the selection
•  Change the action name from Molten Lead to your name
•  Change the action set name from Default Actions to your name

// Use at your own risk!!!
// There must be multiple pairs of files, not an odd number of input files, there is no error checking
// Work on copies of the original files until you are happy with the results
// The original .bmp file will be overwritten
// The alpha _a.bmp files will be closed without saving changes
// Only the top-level folder will be processed, sub-directories must be processed separately
// A selection will be loaded from the RGB composite channel of the alpha data
// An action will then be run to complete the processing using the selection
// Change the action name from Molten Lead to your name
// Change the action set name from Default Actions to your name

#target photoshop

// Capture and suppress dialogs during batch
var savedDisplayDialogs = app.displayDialogs;
app.displayDialogs = DialogModes.NO;

main();

function main() {

    inputFolder = Folder.selectDialog("Please select the input folder");
    if (inputFolder == null) return;
    // Limit the file input
    var fileList = inputFolder.getFiles(/\.(bmp)$/i);
    // Force alpha-numeric list sort
    fileList.sort();

    while (fileList.length) {
        // Digit 2 for two files
        for (var a = 0; a < 2; a++) {
            try {
                app.open(fileList.pop());
            } catch (e) { }
        }

        //var fileCount = app.documents.length;
        //alert("There are " + fileCount + " files to process");

        doStuff();
    }

    function doStuff() {
        try {
            // Select the alpha document
            app.activeDocument = app.documents[0];
            // Select all
            app.activeDocument.selection.selectAll();
            // Copy selection
            app.activeDocument.selection.copy();
            // Close active document without saving
            app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
            // Paste from clipboard
            app.activeDocument.paste();
            // Load RGB channel as selection
            var idsetd = charIDToTypeID("setd");
            var desc146 = new ActionDescriptor();
            var idnull = charIDToTypeID("null");
            var ref59 = new ActionReference();
            var idChnl = charIDToTypeID("Chnl");
            var idfsel = charIDToTypeID("fsel");
            ref59.putProperty(idChnl, idfsel);
            desc146.putReference(idnull, ref59);
            var idT = charIDToTypeID("T   ");
            var ref60 = new ActionReference();
            var idChnl = charIDToTypeID("Chnl");
            var idChnl = charIDToTypeID("Chnl");
            var idRGB = charIDToTypeID("RGB ");
            ref60.putEnumerated(idChnl, idChnl, idRGB);
            desc146.putReference(idT, ref60);
            executeAction(idsetd, desc146, DialogModes.NO);
            // Remove active layer
            app.activeDocument.activeLayer.remove();

            // Now do something with the selection active to limit the effects...

            /*
            // Brightness +30, Contrast +90, Use Legacy = False
            var idBrgC = charIDToTypeID( "BrgC" );
            var desc71 = new ActionDescriptor();
            var idBrgh = charIDToTypeID( "Brgh" );
            desc71.putInteger( idBrgh, 30 );
            var idCntr = charIDToTypeID( "Cntr" );
            desc71.putInteger( idCntr, 90 );
            var iduseLegacy = stringIDToTypeID( "useLegacy" );
            desc71.putBoolean( iduseLegacy, false );
            executeAction( idBrgC, desc71, DialogModes.NO );
            */

            ///////////// Your action here /////////////
            // Action to run
            var actionName = "Molten Lead";
            // Action set to run
            var actionSet = "Default Actions";
            app.doAction(actionName, actionSet);
            ///////////// Your action here /////////////

            app.activeDocument.flatten();
            app.activeDocument.close(SaveOptions.SAVECHANGES);

        } catch (e) { }
    }
}

// Restore original dialog settings
app.displayDialogs = savedDisplayDialogs;

23rd JUNE 2020

Initial code posted

24th JUNE 2020

I have added code for the Brightness/Contrast step to remove the dependency on the action, however, I have commented out the code and left the action in there for now, just in case the action is doing more than this single step...

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

Yes, this is possible via scripting, there are numerous examples for batch processing file pairs in the forums.

 I have to ask why???

 If you are going to save out each layer as a separate layer, why bother combining them as pairs?

What are you doing with the action on the two layer stack, before saving out separate files again? 

P.S. Do you also wish to save the layered PSD as well as the separate layers?