How to separate content for different factions?

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?

They did it by having “modded” crafters. They redeclare the potter for example, and that new potter has a new recipe (e.g. teapot), that the old one does not. The old potter is for the ascendancy, while the new copies from it and adds new things.
I guess it is harder to make an item that is exclusive for the ascendancy, cause rayya will end up copying it,