While I like the theories presented here there's two things the OP got wrong.
Point 6) "Time Crystal" is incorrect. I assume you refer to the "Time Diamond" when you say "Time Crystal" which allows for travel through time, but it's the Time Gear Amulets we get from Tiempa that prevents us from being erased.(Her armor might prevent erasure but that's not confirmed)
As for "Theory 3: Madame X is Marianette" There's a hole in your innitial assesment. Vitus can't be Madame X's Yveltal, because if Melia is suppose to be some alteration of Marianette/Maria then we know this to be false, because of plot we learn in the Narcissa side quest and bits of Angie's past. In Angies past, something happened in which she became corrupted by what I will call "Vitus' Will" so Maria winning after we meet her in Chapter 3 is short lived. we know this to be fact simply because in the Narcissa plotline, we learn in the forsaken lab that Geara's Dad is a man named Sirius, who is revealed to be Vitus, and this is post Storm-9 seeing as Narcissa is an adult when Sirius and Narcissa meet.