Per article ref'd way above this thread (at least that writer's claim) - these were 'pilots' who presumably had trained on bin Laden's (known) 767 training sessions. They indeed reset transponders, IIRC: some just to eliminate altitude data - in other(?) - altered aircraft ID also.
No, the pilot wouldn't have 'helped them' - but he was likely already dead. We can deduce pretty easily that - no way was a 7500 gonna get dialed in (then or in any next). As with all such events: the subtleties are now Out there; at least this batch.
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Ashton