I can't reproduce this, and nobody ever reported it before.
It's not normal the Apply button doesn't change its status normally. It should be greyed out when you enter the parking customization dialog, and it will be clickable as soon as you change a single parameter, indicating you haven't saved the changes. It will be greyed out again, as soon as you press it, indicating your changes has been saved.
I can't find any possible reason why it doesn't work on your system, other than maybe a permission problem in your user account, so you are not allowed to write in the %APPDATA%\Virtuali folder, which is not normal since that's a folder you should always have write permissions. Perhaps the airport .INI file can't be written, so the button wouldn't greyout. But if this was the case, I would guess GSX would display an error, if the file write failed for some reason.
There are no problems using it together AFX, copying & pasting from AFX nodes readouts is exactly what I routinely do to make scenery edits.
