I don't think so, Raphael can be Nightmare. And even if it's the same person, why can't he have two different slots ? It's the same thing than Ryu and Evil Ryu in SSFIV AE. You can play both, it's the same person but they are different at same time : one is normal and the other is dark, and they have different fight styles.
As I said, why do Raphael and Nightmare have so much in common ? Same size, same blond hair, same eyes, and Nightmare pretended to be a noble to the Emperor. I don't think it's impossible.