I'm not sure what you are really asking, you are making it more complicated than it really is.
First, I'll assume you understand this change affects JUST Airport Services and doesn't have ANYTHING to do with Jetways.
Once we clarified this, what this option does, just JUST checking for 3rd party airports that already come with their own custom Airport Service files, and if they are found, they are added to the Disabled list, assuming the best choice is to use the scenery own Airport Services instead of GSX's ones.
Obviously, you are still free to make changes to the list because there might be cases where you would rather use GSX Airport services instead, and the logic behind this is clearly explained in the GSX Manual, Page 8, in the Airport Service chapter.
Nothing is done in "realtime" inside the sim, which is precisely why there's a Config Page in the Installer instead.
If we COULD (we can't) make changes to the installed scenery on the fly, we wouldn't have such options in the Installer in the first place. If we have them in the installer, it's because we can't do anything that affects the list of installed files (either jetway files or airport services files) while the simulator is running.