Photoshop script to export layer combinations

I think I have got the idea of what you want. I find ExtendScript pretty awkward to code in and would tend to do automated stuff outside of Photoshop with more powerful, everyday tools. I would go with ImageMagick and bash. ImageMagick is free and available for Windows, and the basic command to composite two images on top of one another is

convert image1.png image2.png -composite result.png

Of course you can change any or all of the PNG suffices to TIF, JPG or whatever you like.

So, for your question, I have made a sample file with a couple of Groups to show the concept, like this:

The Photoshop file is avilable here.

Zoom into the Layers palette (on the right in the above image) to see the 2 groups I made.

Then go to File->Scripts->Export Layers to Files, and select the options like this:

That will export the following files for you:

layers_0000s_0002_Layer A.png
layers_0000s_0001_Layer B.png
layers_0000s_0000_Layer C.png       
layers_0001s_0003_Layer 1 - Red.png
layers_0001s_0002_Layer 2 - Green.png
layers_0001s_0001_Layer 3 - Blue.png
layers_0001s_0000_Layer 4 - Magenta.png

Note that the format is xxx<GROUP>s_xxx<LAYER>xxx.png

Now you can easily create all permutations of the groups with this bash script. I presume the Windows BATCH file would be pretty similar – though I only do Windows under duress !!!

#!/bin/bash
i=0
# Iterate over Group 0 files
for a in *0s_*.png; do
   j=0
   # Iterate over Group 1 files
   for b in *1s_*.png; do
      convert "$a" "$b" -composite out_${i}_${j}.png
      ((j++))
   done
   ((i++))
done

which gives you these output files:

out_0_0.png
out_0_1.png
out_0_2.png
out_0_3.png
out_1_0.png
out_1_1.png
out_1_2.png
out_1_3.png
out_2_0.png
out_2_1.png
out_2_2.png
out_2_3.png

Just for kicks, I put them all together in a montage and you get this:

Note that if you have 3 groups, you will need a third inner loop in your script, and the command to composite the 3 images together will be more like this (because the -composite option takes the two preceding images):

convert image1.png image2.png -composite image3.png -composite result.png

Alternatively, you may find you can use

convert -background none image1.png image2.png image3.png -flatten result.png