It's an issue where certain features (downloading dlc in Fates, logging into PokeBank) will work but certain others (accessing other castles in Fates, withdrawing/depositing Pokemon in PokeBank) will not work. The PokeBank scenario has been brought up as an issue on the GitHub for it.what issues? it should work just fine on 10.3 U.
I notice that the CFW guide you mention is brought up in that thread too, I'll consider it.