In the Japanese version of Pokemon Diamond, Pearl, and Platinum, there’s a story that references that at one point in history, humans and Pokemon used to intermarry. And, well, we know what usually happens after marriage. Though given the fable-like nature of the Canalave stories, this probably doesn’t mean anything in terms of the game’s canon history, but it is something to think about.
It certainly is something to think about. I think it would be extremely generous to regard these things as being remotely historical without some sort of corroboration (legends about, say, Dialga and Palkia we are compelled to give more credence because of our firsthand exposure to the power of those Pokémon; there’s nothing comparable for this story). We are, after all, talking about what an ancient civilisation believed had happened in their ancient past, so that’s two levels of “ancient past” removed there. Myths of humans marrying animals exist in the real world too and we don’t believe that that means it ever happened. Practically every civilisation has myths of a primordial age when the “rules” were different in some way. I think the existence of those myths says something about the people who told the stories (as all myth does), and the vagueness and offhandedness of what we’re told makes it difficult to say much of that kind. However, I suspect what we’re looking at is an ancient culture that was built (much as the Pokémon world’s modern civilisation is, perhaps more so) around partnership between humans and Pokémon, and had a vested interest in portraying that partnership as equal, regardless of whether that was actually the case.