The Docking system works only if you select the parking in GSX.
I'm not sure which docking system you are referring to when discussion 3rd party sceneries:
- If the scenery comes with its own docking system, GSX won't know anything about it so, it will work (or not) depending how the docking system in that scenery was made. Of course, you can try matching the GSX Stop position to what the docking system is telling you but, again, that doesn't guaranteed the logic (or lack of it) in a 3rd party docking system will match GSX one
- If you customized a default scenery by adding a GSX docking system, or a 3rd party scenery by removing the docking system that came with it and replacing it with a GSX docking system, than it will work like any other FSDT scenery as above, meaning you must first select the parking in GSX before taxing to it.