That's not 100% true for self-hosted:
For applications you can indeed download a copy of the folder from the server and you're done.
For plugins however it's not the case: missing install/upgrade files, resources, javascript, etc. Manually re-creating a plugin's XML file after it's installed is a real pain.
I received some requests for updating old plugins and since they didn't have the original XML file it was a really annoying process upgrading them.