I'll try to give a quick rundown of the recent changes to the default theme. These changes were motivated by a desire to eliminate the complexity of the include hierarchy for the default theme and avoid the upgrade collision problems.
The default theme used to be comprised of files in the blog root and wp-content/. In the root we had index.php, wp-layout.css, wp-comments.php, wp-header.php, wp-footer.php, wp-sidebar.php, and wp-comments-popup.php. Certain files added to wp-content/ would also be used when constructing the default theme. The default theme required special casing in the theme engine since it lived in several different directories rather than within its own theme directory. Default theme files were also subject to overwrite during upgrade since they shipped with WP. To simplify matters, the default theme now lives in wp-content/themes/default. It no longer requires lots of special casing and trapsing through different directories.
To avoid overwrite, a site theme is generated on-the-fly during install/upgrade. If you have old theme files from a previous release in your root, they are copied to a new theme that is named after your blog. A theme header is created and all files are updated to work as a theme. If you are doing a fresh install, the default theme is copied to your site theme directory. This allows you to edit your new site theme without worrying about overwrite during an upgrade. The default theme should not be edited.