GSX looks for the airplane folder and, as a general rule, if you have two models with incompatible doors, it's wrong to share the same aircraft.cfg, because the [Exits] section will surely be different, and this won't affect just GSX. Because of this, GSX correctly assume an airplane variant with different exits, should alway have its own aircraft.cfg, and thus stays in its separate folder.
So, the easiest solution would be moving the MD-11C variant into its own folder, and use aliases to reference all the rest of its files (gauges, textures, panels, etc ) in order not to duplicate any files.
Once the plane has its own separate folder, if you already made a GSX configuration which works for it, it would be enough to rename the airplane folder name under %APPDATA%\Virtuali\Airplanes to match the new folder name you created for the MD11-C variant in the Simobjects\Airplanes folder, so GSX will apply it to the variant only.