FYI I also get "File has been updated outisde of MusicBee" when I rate songs from a remote install.
My setup:
Music Files in network share \\DESKTOP\Music\Organized\* and Library in network share \\DESKTOP\Music\MB on my desktop computer
Main listening area is via a laptop accessing that library and those files over network share
Now Playing is "Playing Tracks" and I usually rate by clicking the stars, which I've added as a field in the track listing.
I've taken to just rescanning the files via "recently played" when I get to my desktop computer. The ratings are there, but MB thinks something else wrote them.
Interestingly, if I rate the files using the android Remote app connected to the laptop install, they do not show up as "Updated Outside of MusicBee" Only the ones I update in the MB interface do.
If I update tags using the tag editor at the laptop, this does not happen. Only if I rate a song by clicking the stars.