As explained in other threads, GSX will instruct to park the center of the airplane (the red cross you see in Top-Down View) in the center of the parking as defined by the AFCAD. This will not necessarily match the scenery lines. GSX HAS the ability to fine tune this for each parking, and we used in some sceneries (KDFW, KLAX) but not at KORD, we'll might update the scenery in the future, especially after we'll release the scenery editor.
The default equipement is removed when you select a parking but, if you play with time acceleration, it will be recreated again by FSX and, in that case, it will not be removed again by GSX.
Some of the ground equipement is not default animated ground vehicles, but static ground vehicles that comes with the scenery. These can't be removed like regular ground objects automatically. Later sceneries like KDFW and KLAX has been designed in a way that GSX can remove those objects, but not KORD. However, if you use the most current version of it, some ground objects have been removed to make space for GSX ones.