That is not the case. Specifically, I saw this at Aerosoft's LLBG, which is installed to aerosoft-airport-llbg-ben-gurion-airport - and conforms.
Please confirm you are still referring to the GSX Config page in the installer, meaning you click the "Exclude 3rd party button" and LLBG is not found ?
Anyway, what I meant with my questions was - must I open the installer and click that button or exclude the specific airport EVERY TIME I install a new airport?
You surely must do that with the "Exclude 3rd party button" every time you install a new airport. Changes to Enabled/Disabled .BGLs cannot be made while the simulator is running, it's not as if we could do it dynamically inside the simulator.
If the new scenery is not found with the "Exclude 3rd party button", then you should add it to the Disabled list by searching its ICAO.