1. WW toys with the idea of gods in story with Aglaecwif mentioning that she was viewed as a god by humans in the distant past....but MC is out here banging her like a normal (monster) girl, we wont know how "godly" any character is until the very end of the game (serious anwser) or until mc gets a chance to bang them (joke..... maybe)
2. Yes the 3rd is the black mannequin looking mosnter that infects you if you one direction when MC gets infected as well as being the one that infected ella, the 4th is the flesh colored mannequin looking monster that transforms into a big tiddy goth gf if you pick the other direction when you get infected, the 4th is also MCs "biological" grandma because Syla refers to her as MCs grandma even if you were infected by the 3rd. The eye is...... well an eye that is 100% not the 3rd or the 4th during the evo into 3rd it specifically tells you to ignore both of them and listen to it. Yes the 3rd/4th are the only pair of twins that want a split chosen so unlike others their infection is more of a mix even if they are directly involved (at least for both mc and ella), however for some (currently unknown) reason MC does have the eye as well so yes there are technically 3 "powers" in MC but really only 2 (the twins power and the eye)
3. iirc Nobody has mentioned the eye directly nor has the MC mentioned it to anybody due to being in a trance it would not surprise me if Ella knew about it because she was more sad than surprised when she sees arbiter MC
4. iirc deus was not attacking the arbiter mc "in front" of him he was attacking him at a previous point when he wasnt unkillable....but now we "know" that deus isnt related to time powers (he tells you this before saying gtfo out of my head and go bang Claudia) so how he was able to do that is a very very good (currently unanswerable) question