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You know, after reading this thread and analyzing all this evidence, I think I finally have a proper conclusion. I'm gonna sound crazy but hear me out:
It was always canon, there's no doubt about that, that much is true.
But it's still a bad move to put this sort of lore into a main game like this unprompted, because the normie audience just sort of have it engrained that Pokemon turn into energy or whatever. This sort of kneejerk reaction is what you'll see from the average Pokemon player, because they've come to understand the Pokemon universe in a way that makes "sense" when in reality it's just a bunch of random bullshit like egg cradles. It'll only hurt the perception the average pokemon fan has of the pokemon universe.
So if giga-autists already knew, and normie players are only gonna get whiplash from this sort of lore dropped on them, why even add it in?