Okay Hippo, first off; Raphael is the captain of the vessel. There would be separate guest quarters for people of note. Second, a man like Raphael would not ever willingly take someone called a Traitor onto his ship, and would never allow him into the same room. Third off, why the hell is a commandant on a smallish vessel like this one?

Edit: looking at your CS just adds more questions. Like how the hell does a pirate become a marine officer when even the Shikibuki are kept at arms length, especially when it says in his personality that he hates the marines? It might seem like I'm ranting, but this makes no logical sense in the One Piece world.