Surely the Transponder and FMC changes could have been made by the flight crew in the "good faith" belief that they were dealing with a "standard" highjack scenario.
Could the "expert" set up of the wing angle on final to get 5 floors not just as easily have been the result of not so expert flying coupled with some "luck"?
Too much guess work - let's all wait for the FDR and CVR analyses before speculating any more.