GSX doesn't change any of the MSFS settings (I don't even know if it's possible from another program), and surely doesn't disable AI airplanes.
What happens when GSX is installed, is that replacement files for all default airports are installed to do the jetways replacement. These files includes parking/jetways only but, if you don't Disable all 3rd party airports in the GSX Config panel, using the "Disable 3rd party" button, you'll have conflicting/double parking spots, which in addition to prevent jetways to work, will likely cause issues with AI at those airports, because the replacement .BGLs are only meant to be used with default airports.