Instead of editing the ‘official’ files you can make adjustments in the ‘community’ folder. That should then persist though updates too.
If you change the ATC_ID in the aircraft.cfg then that will persist when the aircraft is loaded, as long as you haven’t entered any registration number in the world map.
atc_id = “TL-NBR” ; tail number
The black boxes on other aircraft are because Asobo/Mircosoft are too scared to have others see user callsigns due to abuse, name calling, offensive words etc.