>>47515110At the time this book was written, Pokemon's world took place in a world almost identical to our Earth - hence the inclusion of real world continents in this book (and the fact Kanto exists in real life Japan). There was no such thing as "Kalos" or any glimmer of any other region in the creator's minds at this point, except maybe Johto, which, again, is a real life region in Japan.
In gens 1, 2, and maybe 3, yes, real life animals existed alongside Pokemon, but from gens 4 onwards, it seems almost every trace of real world animal references was removed from all parts of Pokemon's lore.
Basically, Pokemon used to exist in a world that was our Earth with Pokemon on it, but now, it exists in a world that is an Earth like planet (but not Earth) with no real animals or continents.