How to Resize a Layer to specific pixel size?

You can use this script to enter a new width in pixels, the height will scale proportionally.

// https://forums.adobe.com/message/11043978#11043978
(function () {
    var startRulerUnits = app.preferences.rulerUnits;
    app.preferences.rulerUnits = Units.PIXELS;
    var bounds = activeDocument.activeLayer.bounds;
    var width = bounds[2].value - bounds[0].value;

    // Loop the input prompt until a number is entered
    var newWidthIn;
    while (isNaN(newWidthIn = prompt("Enter a new width in pixels:", "300")));
    // Convert decimal input to integer
    var newWidth = parseInt(newWidthIn);
    // Test if Cancel returns null, then do nothing
    if (newWidth === null) { return }
    // Test if an empty string is returned, then do nothing 
    if (newWidth === "") { return }

    var newSize = (100 / width) * newWidth;
    activeDocument.activeLayer.resize(newSize, newSize, AnchorPosition.MIDDLECENTER);
    app.preferences.rulerUnits = startRulerUnits;
})();  

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

If you have an embedded SO, editing the SO and changing the .psb file's image size and saving will update the layer size. You can also use the Fit Image command.

Note: I have only mentioned these methods for completeness, they are destructive and you can't resize multiple times as you can with the smart object layer.

When you are in the middle of a Free Transform on a layer you can see values for Width and Height in the Options bar. You aren't restricted to the units that it is displaying. If you selected the contents of the Width field, for example, you could type in 50% or 1000px or 2in or 60mm etc…

I appreciate that you said that you are not wanting to use the Free Transform tool. I thought knowing this functionality, if you didn't already, may change your intended workflow.

What is wrong with the free transform tool? 🤣

I would just open the images seperately and save copies at 1000 x 1000 and drag those in. 🤷🏼‍♂

I suppose you could click with the rectangle shape tool and create 1000x1000 boxes and clip images into those but you still have to scale them 🤣🤷🏼‍♂