If I recall correctly, in the most recent dev stream, they made it sound like the privateer is its own unit created when the citizen is used. As such, the ship's appearance seems to be generic in some way--not specific to a given faction. I could have misunderstood, but that's what it sounded like.
So, it seems it will both confuse the AI and be unidentifiable by human players (as long as they don't see you create it, I suppose).
