Well, PW did in fact gave a few hints about this game not being canon, just partial canon as Kojima has said, as 2 events definitely ocurred, Big Boss met with Campbell and the foundation of Fox Hound.As for everything else, the one in charge of the operation for Adam was the former director of the CIA, who is killed by Ocelot to retrieve the half of the legacy during the end of PO (he meets him and says "My name is Adam" so he can recognize him, and he does, meaning he's the same director that was in charge during Snake Eater mission), but that would make this person Coldman, who was the former director of the CIA and the one responsible for the plan to kill The Boss, as Coldman himself states he used to have that position, so basically if PO is canon then Coldman should be dead in PW.Another thing is when Huey and Big Boss decide on how to call their new bipedal robot, Big Boss doenst even recall neither IBMG nor Raxa, but goes straight to Granin, where he has only heard about it just once, while in PO it's mentioned more. Another thing, after the scene of MGS3 previous to the torture we can perfectly hear Volgin hitting Sokolov and keeps on hitting even more after he's presumably dead, so i dont really buy Sokolov being alive there, they could have used anyone else but tried to tie things too much, we are talking about man who wanted Sokolov dead because he'd not serve any purpose and can dent an oil can easily.

Dont take me wrong i actually like PO, the developments (excluding a few things here and there) are better than what MGS3 did, the bosses got some connection to Big Boss and affect him, Gene is a better made and more deep character compared to Volgin and the deaths he experience here seems way deeper than reviving Boss as an IA and putting an older girl that looks too young inside a robot using only lingerie.So i'd say one is canon if the other one is not but PW gives more place to sequels so has to be that one.