I think that one specifically was a heavily armoured navy brig, but I just happened to run into it at Shieldhold as a positive rep, and the ships are technically free game, you just can’t lay a finger on the marines aboard.
As for some of the other parts, I don’t remember specifically what ships they came from but it’s generally going to be armoured, heavily armoured or above. Most commonly seen on brigs but I don’t see why smaller classes can’t either.
As far as I can tell, only their base health goes up. The parts don’t seem to undergo any upgrades whatsoever. My other command ships are all still packing the wooden or rugged framing, but are about on par to stuff with bronze framing. To this day I haven’t seen any hull armours that actually exceed what’s accessible to players yet.
But with that being said, absence of evidence is not evidence of absence.
Those random pirate factions that can overtake a sea when gravy’s influence is low or dangerously low have actual leaders? Do they have unique drops? What are the spawn conditions?