20:47 - You are correct, the tradition did carry on if a British submarine sinks a hostile ship during her tour. There is a photograph of HMS Conqueror returning to her base flying the Jolly Roger flag after sinking the ARA Belgrano during the Falklands conflict in 1982.
Based on the records what happened is the first ship the Trafalgar ran into was the ship they were disguised as. So of course the disguise ended up being a bit pointless as they'd run into the one ship that would say...wait what? The Carmina was outfitted as an armed merchant cruiser which was intended to allow the self escort of a convey instead of needing to send a gunboat or destroyer.
