No it's the other way around. System refresh will leave all your Metro apps/settings intact, along with your document libraries, and bulldoze/pave everything else. Other than that it should be "basically" the same as a clean install, as far as fucked up registry settings and startup pollution etc. go, but I'm not sure what caveats there might be to that. There's also System Reset which paves over your Metro stuff too, so it's basically the same as a reinstall.