>>35100330As far as I know 3DSes do have unique signatures - their NAND files and console IDs. So the NAND I'm using I believe was located in Russia or something and it will always say I'm in a specific location which I don't think I can really change.
Citra behaves exactly the same as a real 3DS and will write files exactly like a real 3DS.
The difference between a real pokemon and a hacked pokemon is, as far as I know, based upon user error, though using Citra of course I don't have to worry about PGL or whatever that uploading your save file thing is (because if you upload your save file one day and the next day you have 999 masterballs well obvious cheat is obvious). If you want to edit a pokemon, starting with something you actually caught, setting it in all the right places and filling out all the rest of the fields correctly will keep it counted as legit.
I heard that in gens 6 and 7 a lot of the legitimacy checkers got completely BTFO because the data structure of pokemon became sucht that it was really difficult to tell between a hacked pokemon and a real one if they aren't absurdly hacked.