I read differently: When you use the Refresh feature, Windows is still technically starting over with a fresh install of the operating system. The main difference is that the Refresh process automatically sets aside your data, Windows settings, and Metro apps, then puts them back where they belong once the OS is reinstalled. The result is a clean slate for your OS, but with your configuration settings and data intact.
The standard Refresh process will not restore the software you have installed. It will restore Metro apps, but not traditional Win32 software. Microsoft claims this is another function of troubleshooting. It wants to avoid simply re-installing whatever software it is that might be causing your problem.
What Microsoft does is to create an HTML file that lists the applications that were not installed, and places it on the desktop of the refreshed Windows 8 system so you at least know what software you’re missing.