Not sure on Johto, but Kanto, at least, is the name of an actual part of Japan. Tokyo's actually a part of Kanto, as I recall. Geography's not my strong suit, though, so I could be wrong. But if I remember right, Kanto is the southeast chunk of Honshuu, the largest Japanese island.

However, I'm relatively sure there's no Pokemon running around it, so it could be named after a tree stump after all.