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Wouldn’t this have more to do with the human characters though? Rather than the Pokémon?Yes, basically that. I'm not into different characters between different media scaling to each other because they look similar or because they fought the "same character" between the different media (The background story of each individual character is original material for most media outside of a few key components in some material, such as Masters depiction of the game characters being "in-canon"), it's really mostly about the inner workings of the world such as the nature of certain moves or the cosmology as a whole.
The legendaries could be a special case as a lot of them are basically walking lore pieces in regards to the world itself, but even them what is inconsistent will remain inconsistent no matter what, what I say about consistent worldviews is really just about that non-contradicted stuff.
As Masuda himself gave the example, the background lore that Pokémon speak their own name is Anime-exclusive in relationship to the game as that is not the case with the games (Other than a few outliers). Contradictory stuff clearly isn't going to cross-scale (Such as Pokémon saying their own names in the anime, but not in the
games), but non-contradictory general background stuff is officially on the table to be used (Such as the wars in the Pokémon world first revealed in Lucario and the Mystery of Mew).