BOAC,
I think that what captjns is trying to say is that if the PIC leaves the cockpit for physiological reasons they leave behind a qualified co-pilot at the controls. They pointed out that from time to time when said Captain returns there may be a member of the cabin crew sitting in their seat chatting with the FO. In this case there was a qualified copilot at the controls and the Captain remained in the cockpit - just not in their seat.
While I don't condone the actions cited, it is not that unusual for one of the seats to be vacant during the cruise. There does not seem to be any mention of the CPL ever touching anything or doing anything other than keeping the seat warm.
I agree with the other posters who say that if the (now qualified Captain) considered that there was any safety risk they should have spoken up at the time - but clearly they were willing to do something that they believed to be unsafe / against SOP so as to not to rock the boat that was their career. Put that same Captain in another situation where promotion and money have to be balanced against safety and what do you think the answer will be?