OK, one possibility I can think of. At some point, files may have been created where there is currently a mount point which is hiding folders that are still there, on the root partition.
You can remount just the root partition elsewhere by doing something like
mkdir /mnt/rootonly
mount -o bind / /mnt/rootonly
Then use du or similar to see if the numbers more closely resemble the values seen in df. I'm not sure if that graphical tool you used that views the filesystem can see those files hidden this way. So, it's probably worth checking just to rule it out.
Anyway, if you see bigger numbers in /mnt/rootonly, then check the mount points (like /mnt/rootonly/home and /mnt/rootonly/boot/efi). They should be empty, if not those are likely files/folders that are being hidden by the mounts.
When finished you can unmount the bound folder with