today I installed the newest version of GSX and I discovered that I can no longer adjust the parking system or marshaller position independent of the nose wheel stop position.
You still can.
With earlier versions it was possible to move for example the position of the VDGS forward/aft and left right with the numpad keys, and this position was independent of the aircraft. Now when I want to do this the aircraft and it's stop point always moves with it.
I believe you are confusing the fact that GSX now moves the aircraft together with the VGDS/Marshaller and the stop position, as they being somewhat "locked". But that's not the case. You can still move the stop position separately from the VGDS/Marshaller, and the plane will also move back with it so, while you are making the adjustments, the airplane is always in the position it will end up, when guided by GSX.
This is useful if you are trying to align other parts of the airplane (not necessarily the front gear) with the rest of the scenery. WE found it to be easier to use it like this, when we made the hundreds of parking customization at KSDF.
Note that, the editor now is properly taking into account the difference between the front gear and the preferred exit so, the end result will be that GSX will guide ANY kind of airplane to have ITS preferred exit ending up in the same place of the preferred exit of the airplane used to customize the parking.
This is of course more realistic and accurate.
In older versions, you'll always ended up with any airplane having its front gear in the same place, which is not what happens in real life, since different planes will have the front gear in different places, because the goal is to have the main door ending up more or less in the same spot, in order to have less issues using a jetway.
So now, you can use any airplane to customize a parking, and GSX will automatically take into account the difference between the front gear and the preferred exit, which will end up in the same place, regardless of the airplane. That's why there's now a marker on the preferred exit: so you can better relate that, with the surround scenery, usually to a jetway.