This was discussed many times on the forum, the airline code in the aircraft.cfg doesn't affect the ground operator, it would be wrong if it did, because you can't expect to have your home base operators following you everywhere in the world. Instead, the ground operator is related to the airport AND the airline codes of the PARKING. The manual and (more so) the PaintKit documentation, explain how the scoring system works.
The airline code of the aircraft.cfg, has a role, in the selection of the cargo pallet, they are more related to your own airline and, by doing so, we don't end up in funny situations like unloading different pallets than the one which were loaded. Of course, assuming your aircraft.cfg *has* an atc_airline_code to begin with, otherwise the selection will be based on the airport/parking too.