I have exactly the same problem.
I have MSStore Premium Deluxe version of MSFS, and it is not installed in the default location.
I selected to install MSFS in D:\SIM\MSFS
GSX Pro with logging turned on, logs that its reading all the default airport directories from
D:\SIM\MSFS\Official\OneStore\.....
but never logs any of the sceneries I have installed in Community, which is located at D:\SIM\MSFS\Community
%LOCALAPPDATA%\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache\Packages
shows 2 directories (on C Drive)
Community
Official
but if I use explorer to go into those, both are empty.
D:\SIM\MSFS has directories
Community
Official
and both of those have lots of sim packages in them.
Customizing any airport locations in GSX Pro for Community installed sceneries shows that GSX Pro is reading the airport data from the default official scenery path, and not the airport BGL files in Community
Regards
David