Oh, thank you for pointing out /religion_map thingie. I created a sub-sect of Nestorianism, and it had same head of faith, and i wondered why it converted wrong. Now i know.You can mod your ideas to like any other mod. Check the wiki for a modding guide how to add your own or change existing ones.
As for Catholic variants in particular, ifthey have the pope as head of faith, they count as catholic. You can alter that in configurables/religion_map.txt and map them to whatever you wish.