I think that it's likely that what we would call magic would probably be the science of their world, much like Alchemy of the past. A world that was governed by magic would probably develop very similarly to the Pokemon universe. I just know that I can easily go crazy if I try to apply any sort of real world logic to Pokemon.
Mepalo, that's certainly one way of looking at Pokeballs but I don't see how someone who's a simple craftsman could make a nut like an Apricorn into something with its own space and time without magical intervention. Kurt certainly doesn't seem the tech savvy type.
We do it because it is fun to do so.
I'm certainly not trying to devalue the idea of Pokemon theories, I just know how I feel about Pokemon when I try to put logic on them.