I haven't fully understood this method:
To optimize the services of GSX I don't use the mouse anymore but select all positions in the menu with the numeric keys. This is much more efficient than using the mouse.
In any case, remember that GSX Stop positions and GSX Parking position/orientation are things used only by GSX, the simulator itself doesn't know anything about them.
Which means, if you use the standard "Go To Airport" menu of sim to start a flight, you will always have to use GSX "Reposition", which (being a GSX command) will move the plane to the Stop position you customized. It might be easier to start a flight on the active runway, without spending any time choosing a gate, then use GSX menu to select a gate and the "Warp me" function to instantly move there.
The GSX Stop position will also be used by GSX in all cases in it needs to let you know where to stop, be it with a Marshaller or with a *GSX* Docking system.
If you have a 3rd party Docking system, it might be best to have the GSX Stop position matched to where the 3rd party Docking system would have guided you, always keeping in mind that GSX Stop position will use the GSX "Preferred Exit" as a reference (not the front gear ), to have all planes stopping with their Preferred Exit in the same place, which would in turn make it more predictable to have it the jetway working correctly.