Hmmmmm.... Curious... Very curious...
I run W7pro and I've never seen any Compatibility Files button, nor seen or heard the phrase.
I've often wondered what those aircraft folders in C:/Users/(your username)/AppData/Roaming/Microsoft/FS9/Aircraft/ are for. On my rig they are just empty folders with nothing at all in them, while on your rig they apparently contain a cfg file. Very odd!
Since they are in the User folder, I've suspected that they have something to do with multiple user accounts, so that when different users of the same computer log on and start FS, only their own selection of planes will show up on the Select Aircraft menu. But this is just a wild guess, since I have never seen a computer with multiple users that has FS installed. But I can't imagine any other use for empty folders in the User.../.../...Aircraft folder.
What I do know is that when I delete all those empty aircraft folders, nothing is affected in any way. I have read that one should do that from time to time to clean up the system. I have no idea whether that's correct, but I hate useless clutter, so I do it. I can only wonder if it might have some effect if my computer had multiple users and they all used FS9. (Maybe someone who knows will jump in and tell us.)
If I'm right, then we can wonder why MS didn't do the same thing with scenery, since different users are just as likely to want different scenery as they are different aircraft, or so it would seem.
As for installing repaints, the edits have to me made to the real aircraft.cfg file in the real plane's folder in the FS9 Aircraft folder.