Ok, this has been a pretty dead thread, but just wanted to jump back in and say I think I figured this out.
What I did was open an Admin Command prompt in windows and use the mklink command to create a directory link to the DLC folder. This creates a link in the main SimObjects/Airplanes folder that allows the indexer to see the Steam DLC planes as if they were in that folder.
So create the Link, run the indexer, run the panel installer, delete the link.
The only caveat and I'm not sure its even related is I'm now getting a FSinsider.dll error now on launch. But think that is a separate issue that popped up at a similar time.
Here is the specific command:
mklink /D [link path] [target path]
so for example:
mklink /D "C:\Program Files (x86)\Steam\steamapps\common\FSX\SimObjects\Airplanes\E175\" "C:\Program Files (x86)\Steam\steamapps\common\FSX\DLC\364324\SimObjects\Airplanes\feelThere PIC E175"
Be sure after you run the panel installer, you delete those shortcuts in the normal simobjects folder as FSX will complain about having two of the same aircraft installed with the same name since it is looking in both places.