yep, but that did not stop them getting the kites home.
Not at all. The intention was bluntly exactly that. If the pilot was incapacitated or killed if the flight engineer had at least basic flight training he would have a fighting chance to get the plane home.
I recall Saburo Sakai describing a return flight from a raid on Darwin in which one of the G4Ms was having a lot of trouble maintaining position in its formation. After landing it turned out that everybody on the plane had been killed except for, IIRC, the engineer, who had no flight training, and the pilot who had been knocked out. The engineer flew the G4M back to Rabaul and the pilot regained consciousness in time to land it. Apparently the plane had quite an effect on the A6M pilots as they were normally so insulated from the effects of combat, but in this case he said there was blood running out of bullet holes in the fuselage and it was a charnel house inside.