Thanks for the information on flight physics. Since you're in the knowledge of how iron birds flies you should know that when you increase the attitude close to the stall speed the drag also increases very quickly (just look at a polar curve). So why reducing drag with flaps when the AP increases it?
You mentioned that the flaps were retracted to reduce the drag because speed control was critical. If this speed control was so critical why letting the AP spoiling it by increasing pitch (and drag) aiming at a point far beyond the threshold? If one thing was out of control during this landing it's obviously speed.
The shortest way is the straight line, flying above it at pre-stall speed is certainly a waste of energy which can't be balanced by flaps inputs.