Permissions
There may be a permissions issue with flatpaks.
io.bassi.Amberol.json
"finish-args" : [ ... "--filesystem=xdg-music" ... ]
Maybe that should also be filesystem=home
since this would mean that you could play files and folders from Downloads or other general folders. Also consider that playing files with the flatpak version does not work for external USB's, but and that is a popular format of music appreciation.