Gnome-music omits the Music folder if it is a symlink to other location.
19:44 aceler@Compy:~ $ gnome-music
19:46:14 WARNING /home/aceler/Music is a symlink, this folder will be omitted
Yes, Music is a symlink, because I have a small SSD, where /home is located, and a big slow HDD, where all media is located. It is not a rare configuration.
I think, Music shouldn't omit symlinks at all, but if there is a reason for that, not the whole folder.