I don't really understand much about all the files in the Orbiter folder tbh. I was looking through the zip folder that contained the Shuttle Fleet add on. Basically it adds new meshes, new config files, and edits all the existing scenarios to include the new launchpad. I don't know how to stop it doing all that. I managed to delete the config files, but then I was just left with the Shuttle floating in mid air. Even when I tried to install the mid-range launch pad I used to use before I started creating new Orbiter folders for different add ons, it didn't work.
It's kinda frustrating that it's such a good add on, and like you said, the Shuttle itself works great but for some reason it seems you HAVE to also install a really high res launch pad which reduces the frame rate to about 8FPS on my computer. If it wasn't there, I'd easily be getting more like 30FPS when on the launch pad and more when on orbit.