So impressed by the amount of effort you've put into this! Really well done
So as I point the few places I differ please keep in mind that this is in addition to an enthusiastic thumbs up to the vast majority of what you've said:
There should be no restrictions for the choice of a deity.
Yes and no on this. I want to see a one step rule that can be broken. If anyone can worship the lord of murder then Bhaals status as an evil god is diminished. Then alignment just doesn't mean anything any more. Of course we can all think of benevolent aspects of murder -- euthanasia, life changes as symbolic death and all the interpretations of the death card on the tarot. But, the way the realms have dealt with this is to allow aspects to become independent deities -- Lathander and Amanuator are just too different from one another to be aspects the same deity so they gained independent from each other. Same goes for Shar and Sharess.
Now of course, as in the case of Aerie, story trumps all and if a player wants to play as the one exception to the rule that's great. But that character's uniqueness is only made possible by the rule they are breaking. So the game -- like the DM -- would need to acknowledge the strangeness of that choice. Just like they do with drow. A drow wandering in the sun doing good acts is just odd and I'm glad the game acknowledges that.
Tav: I want to know more about your mission.
Shadowheart: I've already told you that information is not for your ears. Let. It. Rest. Besides, as worshiper of Shar you should understand the value of keeping secrets secret.
Tav: Oh, I worship Shar as the keeper and revealer of secrets. You see she also is the goddess of wrongs hidden but not forgotten. Only once these secret wrongs are revealed can the wrongs be ameliorated and a healing process begin. I worship her as benevolent force, Shar holds the secrets that will heal the world.
Shadowheart: That's, that's . . . heresy. There's no other word for it. You can't really believe that?!
Tav: I do. I don't care what the sacred scrolls say, I know what's in my heart.
Shadowheart: So I'm traveling with a heretic. Just when I thought things couldn't get worse. Look, I'm not going to respond this right now but you can be certain we will be having words in the future.
TL;DR -- if you are going to allow the rule to be broken the game needs to acknowledge that. Also, "anything goes" isn't as much fun as are exceptions to the rule.
I have other differences of opinion I'll post later but, again, really impressive work. I hope Larian implements most of your suggestions.