What controls the place where GSX Warps to and the GSX Marshaller instructs to stop, is the "Stop Position", not the Parking Position.
The simulator doesn't know anything about the GSX Stop Position so, when you use the standard Go to Airport menu, it will continue to place the airplane in the center of the parking of the underlying .BGL used by the scenery but, if you use the GSX Warp feature to move there, and the GSX Marhsaller/Docking System to be guided, it will all work.