just to clarify the pokemon games (well at least the main ones, not the puzzle games) are actually the exact same version for all regions, even retail carts, for this reason you can even insert a out of region cart on your system and it would show up unlike any other game which ordinarily would just not show up, the only reason why the retail cart fails to launch on a out of region system is that the update check fails as the update on the cart is out of region....other than the update the game is exactly the same for all regions, and seeing as cia files do not come with updates the actual version users buy from the eshop is region free
TLDR: pokemon is by default region free when installed as a cia, just go grab the update from the eshop and it will work fine