well, we are talking about p3d here. P3d doesn't use the data in p3d.cfg anymore, but ahs its own simobjects.cfg in programdata. That might be the thing?
That doesn't change anything regarding our installers. They never had to change the FSX (or Prepar3D.CFG ) file with the Simobject folders lines, and they don't have to do it now, because it's not needed.
Since the installer adds new sub-folders to the *existing* default Misc folder, regardless where the configuration for its path is located, it's supposed to be always active in any case, since it contains lots of default objects used by the default scenery and the included missions so, we should safely assume that folder should always exists and be active.
If anything, the different location of the folder path lines in P3D compared to FSX, would simply make it the installer more complex IF we tried to "fix" it automatically, in case the users would tamper them for some reason. Which is exactly why we don't even try, especially because the ways files can be corrupted are endless, so it's not very safe or easy trying to detect all cases. Some users would just remove the line, some would "comment" it out, some created "holes" in the numbering of sections, some would have duplicate lines, some could have lines with syntax errors, some might point to non-existing paths, and some even with paths that might exists or not depending on conditions, for example if they are pointing to a removable drive.
So no, better be safe, and don't try to "fix" anything.
If we could create a software that could automatically fix ANY problems in the sim configuration files, assuming it would be safe and not cause other problems, it would be probably more valuable (as a product) than GSX itself...