You can change the AFCAD parking options and even state which airlines park at which gates by using the airline codes in GSX
Yes, but note the airline code in GSX will be used by GSX vehicles only, to set the livery used, but won't be used by AI.
However, they are READ from the AFCAD file, and those in the AFCAD are the ones that drive AI so, if you don't make any changes, they will match, and AI will always use the data from the AFCAD so, provided your AI have been properly set with airline codes in their aircraft.cfg files, they will be assigned to their parkings (provided the parking size is correct, of course), so the type of parking won't matter anymore.