For Team Radiant, this is easy: Since the Rayya’s Children mod only loads when you play Rayya’s children, you can just dump all the content whoch is exclusive for RC in that mod, and you’re done. Maybe you need something the exclude content from stonehearth.smod which is exclusive for Acendancy, but then you’re done.
Except I am not team Radiant. I am a modder who adds in a third mod to alter the game, so how do I perform the same trick?