Yes. I reinstalled OS X on a couple machines do to various issues. I was extremely surprised at how nice the experience is. When I logged back in after the reinstall, Chrome even reopened with my old tabs in it.
If you want to replace various bits of the system, reinstall the OS.
These are different scenarios with different use-cases, and I'd argue it's a much worse idea to conflate the behaviours, as in certain other OSes, than OS X's fault for properly treating them as separate operations.
It's a good thing.