Where has the disk space gone?

[Nick]

Modern computers tend to do this to help prevent fragmented drives and to use the full area of the physical disk inside the drive to even out wear of the surface.

"Modern computers"? - hard drives have no surface wear at all - the head flies above the surface - it never touches (bad things happen if it does). If anything, most operating systems try to keep data physically close on hard drives to reduce inter-track movement by the heads - rotations latency depends only on the RPM of the disk and that is fixed - by positioning data close together, inter-track movement of the heads is minimised and data transfer rates can be maintained. Head movement is one of the few things within the control of the o/s.

Hard drives do not do wear levelling and never have - solid state drives (SSDs) use sophisticated algorithms to distribute data depending on how often its used and how many times the underlying cells have been written - modern SSDs also contain cells with differing capabilities - specifically speed and number of supported writes. The drives also contain a lot of "spare" sectors that are seamlessly mapped in when an in-use sector is unusable due to excessive number of writes or other failure modes.

FWIW, the external view of the sectors of an SSD is a fabrication of the SSD's memory management subsystem and will bear no relationship at all to the physical utilisation of memory within the device.