>>21290894I never considered the national pokedex being divided by regions as an indication of the pokemon being native to that region. That's what the regional dexes are for.
For example, Milotic is in the Sinnoh dex and the Hoenn dex, making it native to both regions. It can also be found in Unova, but since it isn't in the Unova dex, is not native from there.
The division we see in the National Dex just implies that the each of those pokemon were identified first by the professor in charge. That's why the National Dex is "updated" after every generation.
For example, Oak's research group cataloged 151 species when making the Kanto dex, then 100 more were identified after that. Birch's group found a total of 135 species that weren't registered before, Rowan's found 107 other, then Juniper's, Sycamore's, etc.