@Lynn Towle In my experience, there's very little guidance from Microsoft regarding why the default Root sites in SharePoint have the components that they do. That said, I can assert with reasonable comfort that, permissions-wise, there's nothing specific you need to do to your swapped root site to keep the rest of your SharePoint environment working as expected. Our Company Administrator doesn't have any special rights on our current root site, and we've no problems using it.
As for what rights you should set, it's extremely important that you guard full control rights at the root level. Unless what little I've found on the importance of the root site is wrong, deleting that site will make the rest of your sites inaccessible because the root of their site paths is now invalid, and site access won't come back until the root site is restored or replaced. Aside from that, in my view, your permissions should be reflective of your intended purpose for that site.
