This is a common question, and has been clearly explained in the manual at Page 41, the "Understanding the Stop Position" chapter.
Basically, when you are adjusting the Stop position, you should not take the front wheel as your reference, but the Preferred Exit, since the goal of adjusting the Stop position is to have the Exit always positioned in the same place, to ensure a reliable jetway connection.
Since the relationship between the front gear and the Preferred Exit is different for each airplane, having every airplane ending up with its Preferred exit always in the same place, which is what GSX does, results automatically in the front gear in different places, which is how happens in reality.
No, you will not be able to always match 3rd party custom ground markings, since there's no way to be sure they are both accurate AND matches this strategy at the same time. GSX has internally the ability to add custom offset for each parking spot depending on the airplane type, but there's no user interface for it, it's just programming, which we used in some of our sceneries. Even if we exposed this function, it will be very tiresome to use, since it would multiply the time required to customize each parking, for the number of airplane types supported, since there's no guarantee the same formula would work at different parking spots, and surely not across different airports made by different developers.
That's why the current approach of placing the Preferred Exit in the same position regardless of the airplane, is the one that works best as a general approach, considering our main goal is to have the jetway working.
