So the FlightBeam / FSDT installer is allowing for installations outside of the base folder, but GSX doesn't look for those airports
Of course it does. Do you think we would install our sceneries in a way that GSX couldn't find them ?
nor does it have a way for users to manually point GSX to that custom folder.
It's not required, since GSX will pick up the correct folder automatically, provided it has an higher priority of any possible
conflicting scenery you have installedGSX cannot find the afcads of my Flightbeam airports because of this fact.
No, GSX can find the right AFCAD, but if you installed a conflicting scenery and it has an higher layer than our own, GSX will correctly use that one, because it respect the same rules of the sim itself.
If you don't want to be involved in changing the layering yourself, the best solution would be removing the conflicting AFCAD from the other product, when the sim is not running.
You can check which AFCAD is used by GSX with the Parking customization page, then exit the sim, remove or rename the offending file, then restart the sim, and see if GSX is rebuilding the cache. If it's not, select the "Restart and rebuild the airport cache", from the Couatl menu to force a cache rebuild.