Disabling GSX Jetway replacement files is still required, because GSX is not designed to replace jetways at 3rd party scenery, because even with the SU12 Navdata API, it's not possible to replace Jetways dynamically while the sim is running.
To replace Jetways, a replacement .BGL must be made, containing the precise, exact, association between the parking and its jetway (no, it's not "just" a positioning issue, it's a parking->jetway association that must be correct), and GSX comes with about 900 of them, replacing jetways at all default airports, but these are pre-made by us so, hypothetically, we would have to create alternative replacement files for 3rd party airports, which is very questionable from a legal point of view, since we would end up distributing data obtained by using the API to convert 3rd party data, which might have been encrypted too, into another format.
If anything, with the Navdata in use, it's even more important than ever to be sure you Disabled the GSX Jetway replacement files for all 3rd party airports because, while with the old Airport Cache method, GSX at least automatically ignored its own folders when creating the cache, now that it doesn't read any .BGL anymore, it risk to be confused by its own data, if you don't Disable the Jetway replacement when you should.