No quite correct. Airlines don't fly with a third pilot who pops into the cockpit if one of the two flight crew need to pop to the loo.
What happens is a member of cabin crew, who has no flying capability at all, goes into the cockpit whilst the member of flight crew is outside.
This is...
Would the plane not have been on auto-pilot by then so, if the member of flight crew remaining in the cockpit, had been rendered unconscious, the plane would have continued at cruising altitude.