The scaffold includes a parts folder for reusable block parts, a patterns folder for block patterns, and a templates folder for block templates. These are automatically recognized by WordPress and can be used in the block editor. Included is a set of patterns, parts, and templates with an opinionated file naming convention to help keep things organized.
Parts and templates can be overridden in the site editor, which is great for the longevity of a site, but not as great for initial site development. I recommend using the Create Block Theme plugin to copy changes back to the theme files during development. WP Engine's Pattern Manager plugin is also a great tool for doing the same with block patterns.