I am not sure. Currently I am still leveling and don't have a toon at 50 yet, so I don't need to use my ship all that often. I guess that could change once I hit max level.
But that's my opinion, and has nothing to do with what BW said
From what I understood, it will be removable so you can put it in orange gear. I think the set bonus is an added incentive to not just farm one piece of armor and use its mods to put it in every armor piece you have.