What ever I try, I can't get rid of the scenery's default jetways and replace them with GSX ones. I have tried both default and custom profiles.
You are possibly assuming GSX in MSFS works the same as GSX LEVEL 2 in FSX/P3D. There, because of SODE, it was possible to exclude jetways from any scenery making a .BGL with standard Exclusion zones, and programmatically create new jetways on the fly. This required both GSX and SODE in FSX/P3D.
In MSFS, Jetway replacement is made using a very different method, by supplying a set of about 900 individual .BGL replacement files, which are only meant to replace default Jetways at default Airports.
You can't use these files on 3rd party airports because, even if you managed to see the jetways, they won't work, since they are associated to different parking spots (the ones in the default scenery, not the ones in the 3rd party scenery), and that's why GSX by default tries to DISABLE Jetway replacement files at 3rd party airports, if it recognizes the airport due to its name, or let you manually add individual airport to the Disabled list, to disable the ones that couldn't be recognized.
Basically, every 3rd party scenery that has Jetways, should be on the Disabled list in the GSX Config panel.