SM made it abundantly clear that this is more of a Transformers situation than anything else. While back in the first few games the only implication this was true was the simple fact that somebody else could play a nearly identical version of the story to you, although with possibly different Pokemon, sometime between RS and BW it started to become more obvious. BW itself has some interesting implications, with Entralink having you actually sort of visit those worlds, and the implication that in those games Platinum was canonical while DP were technically not. Ohmori's ORAS and SM really just drove this point home. Simply put, every person's playthrough of a game is completely canonical, and perhaps every game they play that they bother to send Pokemon from previous games can also be considered connected in a way, but is only canonical to themselves in a way. I know I brought up Transformers before, and while the continuity family system does work for the more broad franchise and the various mediums, the games are more like continuity clusters, consisting of basically every possible outcome. This also means that technically nothing that's stated as canonical in any given story can be used firmly in any other one. Given how different the anime and games can be on certain topics, this doesn't come as a surprise, but neither is more valid than the other. They each exist with their own universal rules and never the two shall meet, baring some weird unforeseen crossover. I could go on about some of the nuances of this but this is getting too autistic even for me. I will say though this puts apocrypha in an interesting place.
