I've read both the OP's points and yours and I gotta say that I agree on both. While some aspects of the game raises eyebrows, the game never really came off to me as anything sincere in nature and if anything, mocks Christianity in a way (especially when it comes to creating characters where being queer sometimes gets you labelled as "horrible" and a murderer being "redeemable" depending on how you made your character). Imo I think the game doesn't really take itself seriously at times, judging by most of the game's dialogue, especially trait descriptions. If the game is problematic as people say, it'll be quite obvious from the start.