Besides PKHeX. Maybe if I create a Pokémon X and Y editing program of my very own later on. Would be something that I'd consider doing on my own. Unless I need a little bit of team work involved.
The prices are very high on those websites. But it'll be a waste of cash anyways. And if you want to look at a low price range of products. Go to Play-Asia
Yes. The saved game if it were far anough. Has to have the Pokedex. Correct. But if you want some pointless items for extra. Then use a Japanese 3DS as well as the others
Or if you just have the Cyber Save Editor and a JP X or Y cart. And have Pokemon Bank on your North American 3DS. Then you should be good to go. Because obviously that's region free