there should be no add-on.cfg entry created it will be added by p3d to appdata once p3d runs and it finds a folder in my documents \ prepar3d v4 addons
It won't be added, and no question will be made, if there's already an entry for the same add-on in the add-on.cfg under %PROGRAMDATA%\Lockheed Martin\Prepar3d V4 so, under normal circumstances, you will never see two entries for the same add-on in the two add-on.cfg files.