OrbX adds TEN of THOUSANDS .BGL files in those two folders:
FTX_VECTOR
FTX_OLC
And, as of today, nobody ever reported they ever contained airports (AFCAD), which seems to be consistent with the naming, since one folder seems suggest it contains vector data (coastlines, roads, rivers, etc.) and the other it's Landclass so, nothing to do with airports.
So, in order to speed up the cache regeneration time, GSX automatically skips those two folders.
So, it's entirely normal you won't find anything related to these folders in the scenery.cfg used by GSX under %PROGRAMDATA%\Virtuali. Note that, this file is CREATED when the GSX scenery cache is generated so, it's the *result* of that process, not the *source* of it.
Have you tried the "Restart and rebuild the airport cache" option ?