You assume making religions "linked" is actually easier to code. I'm not saying that it is or isn't, been too long since I looked at that database structure, but chances are it's not actually reducing the implementation effort even if it is conceptually "simpler"
Basic idea was inside a religion is a "sect" (so for Christianity you'd have Roman Catholic, Lutheran, etc.) and nobles can choose to join either the main line religion or one of the "sects". Would it be easier to just add sects but not schisms until a good way of implementing the schism is decided on?