I am not from Laminar Research; just a flight simmer that does not support the steam version.
Steam is a 3rd party hybrid version of the official X-Plane version from Laminar Research. Steam will not integrate with the Laminar Research version.
Not having installed steam, from what I have seen and read in this forum it installs differently to the recommended installation method of the official X-Plane version. From your own research you have found the file structure is different resulting in your current dilemma.
I would suggest you seek assistance from a Steam forum.