I think you're missing my point. The institutions are necessarily the way they are due to the texts/beliefs/beliefs in divine revelation that are central to the religions. I'll grant that these are not the only possible readings of the text, but they are a plausible reading and one that can be expected to take place. If there is divine revelation, the revelation must be made in a language, language is imprecise and the more voluminous the revelation the more opportunity to interpret. By asserting that you know what god (an unverifiable entity) wants, you are necessarily giving cover to all others who make this claim. You are giving more cover the more similar the claim is to your own.

Catholicism: I understand that you are in some ways familiar with this religion because of your upbringing, but I think that may also be clouding your understanding of it. Firstly, intelligence does not necessarily generalize to all aspects of cognition-- there are indeed very intelligent people who happen to hold very stupid beliefs. Second, insomuch as a Catholic does not literally believe in transubstantiation, they are not Catholic. You can't play this game with Catholicism. It is a hierarchical religion, the Pope receives direct dictates from god, and these dictates flow down stream. The church dictates the set of beliefs that together make a person a Catholic, and they have made it clear in no uncertain terms that transubstantiation is not a metaphor.

I like Catholicism as an example because its hierarchical structure makes things clear. However, if you want to play this game with a religion with a distributed authority, it just takes me a bit more work. The short of it is that we can go tenet by tenet and in the end the individual either believes their religion makes a suitable claim, based in faith, about a testable proposition regarding reality, or when we get to the bottom of it words mean nothing if they wish to keep calling themselves a member of whatever faith they claim.