Uninstalling GSX and replying YES to the question "Do you want to remove the Addon Manager?" should normally remove the GSX Simobject entries from the FSX.CFG file.
This removal happens only when replying YES to that question, because if you had other FSDT products installed and you wanted to uninstall just GSX, removing the entries upon GSX uninstall would cause the other sceneries to stop working as well.
Also, reinstalling GSX should update the existing lines to the current settings.
HOWEVER, you said you have a custom FSX.CFG file so, it's possible that the installer didn't touch it, because it either had errors or included things that are considered illegal in .CFG files, which are in fact .INI files. For example, C++ style comments ( // ) are considered illegal in .INI files, although a proper syntax is not really formalized, since .INI file are not really structured so, some use the semicolon sign to start a comment, others use the // method and, since it's quite complex to deal with these changing styles, the installer won't try to update/modify a file that it consider not legal, which might explain why the entries weren't updated.
In any case, thank you for having posted a follow up that might help others.