Some further information, having tested some more (since I did not test completely thoroughly before). It seems that when starting a flight in the air, the tail number spoken is the one in the aircraft.cfg, but if starting on the ground (in the same aircraft, livery etc.), MOST of the time, the ATC options work as expected, i.e. tail number, callsign and flight number are spoken as set in the world map UI. There is the odd occasion, however, when it is still ignored and it defaults to the options in the aircraft.cfg file despite having not changed anything.