I have the suspicion, however, that there will be nothing as simple and off-hand as "Sophia and Azeyma are one and the same." I suspect that SE has plans for the Twelve in the future that are much more complicated and involved than just the occasional off-hand, "Oh, yeah - this one Elder Primal was actually one of the Twelve." It would be odd, too, for Sophia to be one of the Twelve, but the other two of the Warring Triad were not.

Not to mention the fact that, in theory, roughly a twelfth of the player population are technically WORSHIPERS of Azeyma, having chosen her as their patron deity. How are those people supposed to feel about the revelation that their deity was actually just another primal - and worse, that they have to fight and kill her?