Citra sadly can't directly change subregion settings and even country sometimes is buggy (I set to Italy but the games read it as Russia), but using System Settings app worked.
As far as I know, PKHeX can emulate local trade. So if you have one PKHeX tab with your original save file and another with a one of these save files and you move a Pokémon between them it's like a real trade (with right memory, last OT, etc).
Find US version of System Settings app is easy (just google "3ds system settings app"), but I didn't find the japanese one.