The command hsm factoryReset (which can be run from a local serial console only) affects only the HSM, and not the settings for other components of the appliance.
The command (sysconf config factoryReset) affects appliance settings external to the HSM.
To bring your entire Luna SA as close as possible to original configuration, as shipped from the factory, run both commands.
"Original factory configuration" is an approximation. If you have performed firmware and software updates, those remain in place, and are not affected by the commands described above. The reset commands (above) affect contents of the HSM and settings of the HSM and the appliance that contains it. Reverting of software and firmware is outside the scope.