Although I've used the script to update without issue a few thousand times, some feel it's safer to only update from base (in case an extension is still in use when reinstalling something). Worse case scenario is that a reboot will be necessary, although I've never even had to do that. Update removes symlinks and umounts tcz's & handles icons/menus before updating.
Scripts have the advantage of easy updating, although not everyone will know how to use them.
re: tcz-uninstall; same issues. It's in the archives, and probably a lot of us continue to use it.