The problem is not df, that one is correct. The issue is the myriad of symlinks that get counted multiple times when showing the graphic version. This is because the way Nethserver works, /home is the same as /var/lib/nethserver/home and the same fun happens again when you use FTP with system users, as this will utilise home aka /var/lib/nethserver/home again.
The df command is always right, the graphic might be wrong due to following symlinks or bindmounts while aggregating the files in those folders. If you could make it so that it ignores symlinks or bind mounts, this issue should resolve itself.
Sorry if I necromanced this topic, I called it in as question, and got referred here.