The whole Matoya thing is apparently fairly simply logical. With Y'shtola not currently inhabiting her body, Matoya is able to take it over. My friend recently played the BLM questline in SB and said that's already established to be possible.
Minfillia will be the curious question to see answered, but a reincarnation makes sense either way it works out.
Regardless of what's coming, I get the feeling our next few MSQ patches are going to have a LOT of story with some surprises in store.