GSX doesn't change how your airport is named. As you have noted, FSX has limitations in the names that can be used, so all default airports and 3rd party airports have to compromises to fit the real world definition to the FSX implementation.
We fixed this, but only for our airports, see for example JFK or KLAX, have more descriptive terminal names, but it can only be done for airport when there's a specific customization, like all the FSDT ones.
For any other airport, what you see in GSX is exactly the same that you would have seen in the defautl "Go To Airport" menu so, the problem of having to relate it to the real world names would be exactly the same with GSX as that with FSX alone.