By default, PMDG have Door 2L opened on the 747v3 (Cold and Dark). Door 2L is their convention.
GSX won't begin to board or deboard passengers until Door 1L is opened.
There lies the problem.
But this is an entirely different issue then. You are suggesting that it might have been best if we considered the PMDG "L Entry 2" door as being the Main Passenger door rather than the PMDG "L Entry 1", that might be something we can further discuss, but it's NOT what my reply was about.
What made me suspect you still have another GSX.CFG file interfering, is that, regardless if the 1st or 2nd door was considered the Main passenger door, it SHOULD be called properly, with the PMDG-styled name, because that's how we configured BOTH of them!
L Entry 1
L Entry 2
NOT "Exit 1", which is the GSX default name for the 1st Door on the left side of a default airplane or a plane that hasn't been configure yet, and surely not "Door 1L" or "Door 2L", which I think is a terminology used by the CLS A330/A340, but I cannot see how GSX could confuse it with the PMDG 747-400.
Now, about the issue if it might have been best to use the same PMDG "standard", it's not so simple. Right now, GSX always considers the 1st Passenger door as being the "main" one. This because the parking might not have a jetway, and on an apron, you would surely use the 1st door, together the the related stairs.
So, I guess a more flexible approach would be allowing for another OPTION in the airplane configuration editor, to automatically SWAP the first two passenger doors, if the parking has a Jetway, which is something we might surely add.
In the meantime, if the majority of the parking spots you use it's on a gate with a Jetway, you can swap the doors in the configuration, by copying all the parameters (pay particular attention to copy everything, including the custom XML expression) from the Passenger Door 2 into the Passenger Door 1 and Vice-versa, swapping them.