The best way to fix that is to create your own AFCAD with a revised altitude, suited to the adjusted ORBX vector altitude. Then GSX will read this new AFCAD instead of the old default AFCAD and put the gates at the correct altitude.
Sorry, but that's *exactly* like disabling the airport in the AEC tool.
The issue is not "GSX not reading the correct AFCAD", because GSX obviously does. The issue is that GSX doesn't read an AFCAD if it's not a complete airport.
OrbX changes the default elevation of an airport, by adding a very small AFCAD that doesn't contain *anything* other than the elevation change. GSX won't use it, since it's not an airport, there's nothing there GSX can use, and GSX always read one AFCAD at the time.
By disabling the airport in the AEC tool, the small altitude correction .BGL is disabled, so the airport goes back to the altitude set in its own AFCAD, which GSX can use.