Honestly, I would be surprised if we ever actually saw the commander's face. I'm not sure that the game would be hurt if you never saw the Dragon Commander. Walking around would be nice, maybe, but if the only time you get to walk is around the ship, eventually you might get bored and just want to warp from room to room.
I think walking around the ship would be important to give the player a sense of place and, dare I say it, immersion. If it's just a glorified menu screen navigated by a disembodied entity (who is supposed to be the player character), I think there would be a disconnect. And so the incentive to roleplay would be diminished and the temptation to just min/max the system would increase.
Also, Dragon Knights are not full dragons. I think it would be... important... to show the Dragon Knight outside of combat in order to demonstrate that, well, they're not full dragons.
Though speaking of combat, I wouldn't mind if the Dragon Commander was not dragon-shaped all the time. Maybe when assaulting a rival's castle or something, the available space becomes too small for the dragon form to fit. Something like that.