You're right, not everything needs to be visible for a UI to work. But it could be if it were properly designed and had a visual diagram. It would afford the user less work to manage the program. It seems like a good idea to me.
The design is going to be app-dependent, and out of Microsoft's hands. The Start screen itself, for example, is used in about 99% of instances to view information, launch programs, or search for content. Since people don't spend much time customizing, that option must be toggled into view. Certainly there are programs that would benefit from a larger number of exposed tools, and others that exist primarily to display content. I think the Metro environment has as much influence on sensible design as the desktop environment does - the latter in which you'll find graceful UIs and others that look like train wrecks.