Comment 8 for bug 1335384

Right, after changing a UID it's your responsibility to walk over the entire file system and change files/dirs accordingly. This definitively does not just affect /media/, but also quite some files in /var (/var/spool/crontabs/, /var/lib/lightdm-data/, possibly /var/mail/, etc.). So if anything, this should be a wishlist bug against usermod to offer scanning the file system and change them; usermod already does that for some known files, but not all (and the manpage even says that you have to do it manually).

That said, there's some room here for udisks to adjust UIDs of existing /media directories on mounting when it sees that their names and UIDs don't match. It's less obvious what to do with changed GIDs as that might be a deliberate configuration.