Performing a factory default will restore the appliance to the version stored as the factory image. If the appliance has been in-place upgraded, the factory image won't be the same version as is currently running.
A clean install (via CPUSE) will create a fresh install of the selected version, but the internal hard drive is not formatted or re-partitioned.
A clean install via USB will format and repartition the hard drive wiping all data off the internal hard drive. It will also create a new factory defaults image matching the version installed.