It's a possibility, though as others have said the specifics remain unclear. If Y'stola's body remains an empty vessel, there's nothing stopping Matoya from possessing it... somehow...
It clearly is Y'shtola's body, though, with the faded white eyes.
Alternatively, I would posit that "Matoya" or perhaps "Master Matoya" is simply a Sharlayan title, and for whatever reason Y'shtola inherits it before the beginning of Shadowbringers.