Well, I met the Ark Royal in the campaign, long before I downloaded anything via UPlay. And I'm quite shure, this WAS the model of the HMS Ark Royal, neither a proxy of the HMS Illustrious, nor that of any other ship.
AFAIK a ship appears in the campaign if it is either determinated as a specific unit or as a random unit from a group class (here: Fleet Carriers, UnitType=9). Everything that is needed to show up a working unit of HMS Ark Royal is included in the vanilla game. So the game displays randomly one of these units defined as type 9 (Ark Royal, Courageous, Eagle, Illustrious etc.) if the mission contains a random generated naval group with generic fleet carriers.
I haven't met the RMS Queen Mary yet, therefore I can't say, if she's using a proxy of NAMC_Rawalpindi in the campaign. But if this should be the case, it would be possible to edit the mission files of the campaign with MissionEditor and link the appearing passenger liner to the model of NPP_QueenMary, as this model is included in the vanilla game with all it's functionality. Otherwise she wouldn't appear in a single mission, but she definitely does.
Oh, and of course the UNIT appears, not the FILE. You're right, my last posting has been mistakable.