GSX treats all airplanes sharing the same aircraft.cfg as one. This is precisely to prevent having to customize every single livery when nothing except the livery changes. This because the most common case of a multi-livery aircraft is like this:
A root folder in Simbojects\Airplanes\AIRPLANE_NAME containing the aircraft.cfg file, which is shared by multiple liveries, which are made by having multiple [Fltsim.XX] sections in the aircraft.cfg, so they all share the same configuration, except for the livery. This is the more common case.
If multiple liveries are made by having multiple root folders, each one with its own separate aircraft.cfg, like this:
Simbobjects\Airplanes\AIRPLANE_NAME_LIVERY1
Simbobjects\Airplanes\AIRPLANE_NAME_LIVERY2
Simbobjects\Airplanes\AIRPLANE_NAME_LIVERY3
GSX treats them as different models because, it's assumed if they don't share an aircraft.cfg, they ARE different. Sometimes the difference might not be enough for GSX to matter, like different engine brand placed at the same position, or variations like winglets/sharklets, etc. but usually if the aircraft.cfg is different, it's because of changes that DO matter to GSX, like cargo variations with an entirely different doors arrangement.
That's why GSX treats airplanes with separate aircraft.cfg file as different versions, which must be configured separately.
Usually in these cases, since many parameters might be similar, what I usually do is to edit one model first and, when it's done, I create a new folder for the other variation in %APPDATA%\Virtuali\Airplanes that MUST have exactly the same name of the root folder in the Simbobjects\Airplanes, and I copy the GSX.CFG file from the folder that I edited for the first variation. Then I load the variation, check GSX is reading the new copied config, and I'll eventually edit the differences, which is faster than redoing everything from scratch.
