I would suggest to first add ALL the airports you have via Addons Linker, then do the steps to exclude 3rd party airports for GSX, and then work with Addons Linker to remove airports you don't need in your current session.
I'd only configure GSX in the Installer if GSX gets an update or if I install a new airport (in the latter case, adding the exclusion manually is easier, no need to rescan all).
The Jetway exclusions don't matter if you're not flying from/to these airports in your session anyway and doing these scans for 3rd party airports is pointless work to do every time.
If you disable airports in AddonsLinker for performance/stability reasons, you don't need to adjust the exclusions in GSX every time, they just don't matter.