Its nothing to do with the different console, its to do with the version on the console, even though EmuNAND is 6.3, its still running through 4.x, so its using the old KeyY method, where as a legit 6.3 system is using the new KeyY method, which involves new flags and a totally different keyY crypto, If you played and saved on a EmuNAND, you could play that cart on any other 3DS via emuNAND fine, however it wont play on a legit 6.3 system as it expects the new Crypto, which isnt there, Vice versa if its been played and saved on a 6.3 3DS, it wont ever run via EmuNAND, but will play fine on any other 6.3 system fine, the EmuNAND is in fact really your original system version masquarading as the newest firmware