I can see how that would happen. I think it might be better for me to check what the permissions should be for first install, versus what they should be going forward, and maybe change that task up a bit. It might also be something that was required to work around an issue in earlier versions of Drupal and is no longer needed in the first place (simple is always nicer!).
I'll try to take a look at this and see what I can find by the next time I update the book.