Actually I think there would be an easier solution.
Consider the example shown in the attached screenshot. This is Gate 7 at SAZS by SimulaciĆ³n Extrema, which is installed in my community folder, and GSX reads the correct AFCAD file. Still you can see that the passengers are walking too low along the jetway, so their legs stick out the bottom (cf. red line) So GSX obviously interprets the height at the airplane correctly, but not at the point where the jetway is connected to the building. I tried to fix this by adding 3 custom PAX waypoints: One at the connection between the bridge and the terminal, one at the end of the bridge and one at the jetway connection to correct the height. Unfortunately, what happens is that the passengers walk along their original route for the length of the jetway and then "step up" to my last custom waypoint. If instead my last custom waypoint were taken as to replace the point where the passengers go automatically, everything would be OK.
Maybe it's possible to include it as an option that the last custom waypoint replaces the automatic second waypoint? I agree the first automatic waypoint should remain bound to wherever the aircraft is.
Consider also a second example, shown in the second screenshot. This is Gate 4A at EDDH by Aerosoft/sim-wings. Since this is a marketplace scenery, GSX can't read the AFCAD file and is using the generic file instead, so all the gates are way off. I am trying to salvage what I can through manual customization, which for the most part works pretty well. The passengers, however, seem to float to some point related to where the jetway would be in the generic file (which is rather Gate 4B than 4A). I thought that by customizing waypoints up to the jetway connection (as indicated in the screenshot) I could make the passengers walk through the correct jetway, but it turns out that they still follow their automatic route before floating back to my waypoints - so all the custom waypoints have just been added, instead of replacing the wrong ones.