it looks like it is possible to show a link in the backend of WordPress during an upgrade which will contain a zipfile of just the changed files for that version.

This solves my concern that we discussed on Twitter, which means that there won't be overt promotion of multiple upgrade methods. Having just a link within the administration panel is rather minor.

Auto upgrade should be the primary upgrade method with uploading only the changed files coming in second. Last would be replacing all of the files.

It was always my assumption that auto-upgrade was replacing all of the files. If it's not, does what occurs during an auto-upgrade equate to what occurs with "uploading only the changed files"?