I think this feature needs to be looked at again - and reworked. In my first game with them DISABLED the entire HRE converted to Orthodox. The problem is that the ruler can still secretly convert and personally adopt - and then convert his followers but with Secret Religious Cults DISABLED vassals can't convert back to Catholicism as easily. With the option ENABLED the problem is worse as realms keep switching religions all the time. So neither option is good at this time.