It's opaque because it isn't clear where the files are located on the fs; and you get confusion or strange behavior: if I delete the media library file, will the fs version also be deleted? What about the other way around? And how does that work for renaming or moving? Etc. etc.

I think a tool should embrace the filesystem as much as possible. If metadata doesn't fit in the fs view, then perhaps store them in hidden files next to the actual files. Needless to say, if these files are not there, the system should deal with that gracefully.