I'm not 100% too sure as I have only touched programming. but I'm pretty sure you just tell the AI to use the same mods available to the player by altering ' Index.ini in Base.rte and also messing around with the Activities.ini)... by doing this you can ass which ones load for the AI and which don't. the only problem is making a nice little program that will alter these for ya correctly.
I know there is a link on how to mod the startup to give the AI the ability to use Modded units, weapons, dropships. I can point you to this page which seems to have narrowed a lot down (I still cant understand it 100% though) http://www.datarealm...tivities.ini_Editing
I tried it once to give the AI dark clones and crashed the game unfortunately, hope that you have a better head on your shoulders than I do. My specialty is animation and unfortunately not programming. I'm pretty sure someone could tell you more on the cortex command forums.
I will understand if it's a bit too much work but maybe you would enjoy the challenge and I'm Damned sure a lot of people are going to love you for it and pretty sure it will even make it into the final game.
Thanks a mil in advance