Then why wouldn't the pilots then radio "MAYDAY, MAYDAY" or something like that alerting others that their plane has been commandeered?
Because now the first priority is to fly the plane then make the call when you get everything back under control. Mayday calls have been moved down on the list so as to not distract the flight crew from the immediate problems.
Because a flight engineer with a laptop could disable everything, system by system. He’d be ‘remote’ flying the craft from inside the cockpit.
I believe the computers engaged the change of flight path AFTER the ‘alright, good night’ comment. Perhaps all comm was disabled at that point, as directed by the modified software.