I've seen people say it wouldn't make sense for Matoya to possess Y'shtola's body, because if Urianger is fine, why wouldn't she be?

I personally believe that Matoya indeed did take over Y'shtola's body. It could be that Y'shtola was unable to return due to her circumstances surrounding her "aethersight", or just runs out of time between her waking up and Shadowbringers.

The situation being as dire as it seems to be, I feel it's very plausible that Matoya would borrow Y'shtola's body because her skills/knowledge are sorely needed.

It would also explain her going from a Conjurer to a Black Mage.