Personally (I am not playing around with the definition of the word "canon") I think that FMC in P3P is canon but does not apply to the main timeline of the series.
Obviously Atlus chose to have male MC in the timeline of Persona games and thus, all the games will refer to him and not the female mc.
That said, female MC still is canon in her own timeline that so far didn't really expand and probably won't. That does not mean she didn't exist. She is just dead end, something like... I dunno good analogy... Like non true ending of the game. It can and if you want to, does happen but only the True ending has continuity in the series.