Auto upgrade replaces all the files, and likely will continue to do so. It's good practice, as it is the best way of ensuring that you have a clean, complete WP install.

The "changed/added files only zip" can be downloaded manually from Trac by people who cannot use the auto-upgrade, and who don't want to manually upload an entire WP install when only some of the files have changed. It's not going to be a canonical upgrade method — it's just a handy shortcut for a small group of people.