Seriously, and I mean this in the nicest way possible (as in I think you should seek help if you aren't already and I wish you all the best), but I really do think you might have some sort of schizotypal personality disorder. I know because I do as well and sometimes think I see strange patterns where there aren't any.
When I said that I don't believe it has much of a place in the modern world, I meant it in term of a country's official policies, and I hoped this was clear already from the context. People can believe whatever they want really, but I don't think religion should have any kind of influence except on the individual practicing it, if they so choose to.
That doesn't mean it shouldn't feature in games, if it's ONLY used by people to try and create interesting story elements. The reason why it is included so heavily in this game is because I generally find occult themes interesting, and which is also why all these mentions of religion that you bring up are excerpts from the Old Testament that, again, really do focus on some of its most gruesome aspects. I know it is not something that exists in the official Harry Potter universe, but then this also isn't the official Harry Potter universe, it's literally just a porn game with a bit of meandering fastfood philosophy sprinkled in there.
I looked through your comment section to see what's up with you, and found a comment on a game with weird sadism towards woman in it, in which you made quite the correct observation about its weirdo author, that people don't spend months and months creating a game whose elements they aren't personally interested in. I want you to now apply that same logic to me when you ask WHY. I simply enjoy those elements, alright? I don't find religion to be a particularly good idea, but I love everything from the Old Testament for HISTORICAL reasons. It's really as simple as that. Honestly I felt that I was being a little TOO anti-religion and inserted the priest character, the muslim prayer room, etc to create a bit more of a balance.
A little further in the game, you will find that the main bad guys are literally Old Testament Yahweh / Baal worshippers, who, again, energetically discuss certain sacrifices. I think I'll leave that as the closing remark on my "proving" that I am not some religious nut secretly trying to insert some secret, religion-positive message into a porn game of all things. If anything, I leant a little too much in the opposite direction for my own liking.
About the character faces, I don't know man, those are the only 5 examples and they all look like what you could reasonably expect teenagers to sometimes look like. The only really feminine guy is Fabian, and, to a degree, Barry Jenkins (the red haired guy in the pics), but those are entirely intentional.