Also, when one of three is incapacitated, is it safer to fly with both pilot positions occupied and FE post empty, or with FE post occupied and one pilot seat empty?
In my opinion, formed from 7,000 hours in 727s, I would definitely say the left seat and the FE seat to be occupied in that situation.
Come to think about it, I've flown with some co-pilots (okay, okay, FOs) that for all intent and purposes the right seat was empty.
In fact on one takeoff in the 727 the FE may have saved our lives. When I called for the first flap reduction, at 500 feet AGL, the guy in the right seat put the flap handle to full up/clean position. The FE saw him do that and yelled at me to get the nose down and start building up airspeed, then the FE put the flap handle back to 10 degrees. To be honest I don't know if we would have stalled or not, but that was not the place to find out. It was a hot day and we were at gross for the conditions.
Yes, the co-pilot bought all of our drinks that night and I paid for the FE's dinner. Actually the guy in question turned out to be a really good pilot, that was like a wake-up call to him.
Oh, one other thing, after this we changed our procedures to first flap retraction at 1,000 feet AGL.