It seems likely either that XFS has used the disk space for snapshots or that there are a significant number of files hidden under one of the mount points

I'm not familiar with XFS so I cannot offer advice on checking snapshots. However, for the latter, try this:

mkdir /mnt/root mount --bind / /mnt/root du -hs /mnt/root/ 

I suspect you have a lot (an awful lot) of data hidden under one of the boot, dev, run, sys directories that's usually inaccessible due to other filesystems being mounted there.

If the du returns significantly more that your reported 6 GB used then this is almost certainly the issue. Use this to identify where the missing files are hiding:

du -hs /mnt/root/{boot,dev,run,sys} 

Remember that /mnt/root really is your root / filesystem, so treat deletions or other file manipulations with great care. In any case do not try to delete any directories directly under /mnt/root that might be used as mountpoints.

It seems likely there are a significant number of files hidden under one of the boot, dev, run, sys mountpoint directories that are usually inaccessible due to other filesystems being mounted there. Try this to access them from your running system:

mkdir /mnt/root mount --bind / /mnt/root du -hs /mnt/root/ 

If the du returns significantly more that your reported 6 GB used then this is almost certainly the issue. Use this to identify where the missing files are hiding:

du -hs /mnt/root/{boot,dev,run,sys} 

Remember that /mnt/root really is your root / filesystem, so treat deletions or other file manipulations with great care. In any case do not try to delete any directories directly under /mnt/root that might be used as mountpoints.