In-file FLAC ratings are not supported
With lollypop set to "Save changes to file", MP3 ratings are properly read and written. But FLAC ratings are not. For example, here are the tags of a sample FLAC file, as seen by NTag:
The RATING=80 tag represents a "four-star" rating. Note that there is no official standard for FLAC ratings, but this is a pretty common one: 0-100. In this case, these were written by MusicBee on Windows.
If you agree with this, I'd be happy to contribute a PR to implement it. A few pointers on where to start looking would help