Your method is far too painful...
The scenery.cfg in the Couatl folder is generated by the Addon Manager, and it's used only by GSX to keep track of all scenery areas (the sim won't use it) but, since Couatl can use it regardess if the pathnames end up with \scenery or not, we posted an update of the Addon Manager .DLL, which can be obtained with the FSDT Live Update now, so pathnames will not end up with \scenery anymore, so if you fool 3rd party scenery utilities to read from there, instead the default place, it might allow them to work, at least until they will update them to support the new method properly.
Now, if you find that ANY of these utilities will ever corrupt this file, please do not hold us responsible because, if they do, nothing from FSDT will ever work and GSX would stop working everywhere.