it was evidently not considered by the captain that the flaps could be in an incorrect position, or at least, didn't enter his thinking at the time.
The evidence for BEA 548 suggests the captain was experiencing a major coronary episode at the time, and from that point onwards without a CVR we'll never know exactly what happened. All we have is that the leading-edge droops were raised while the aircraft was travelling some 60-odd knots slower that the airspeed they were supposed to be raised at and at that point the cockpit warnings would have been somewhat overwhelming, and that's without taking into account the fact that the PF would in all likelihood have been completely incapacitated.
So many accidents have been caused because a basic mistake made while pilots were distracted, fatigued or even incapacitated snowballed into an unrecoverable situation within seconds. I guess this is the reason for "sterile cockpit" rules for certain phases of flight.