to summarize previous discussions:
what should be done is to have a top level "Bookmarks" folder, BUT in the UI, don't show it to the user. it would be merely for API compatibility.
this is because that bookmarks folder doesn't need to actually do anything important in terms of organization.
the other special folders, Favorites and Bookmarks Bar, should show up above all other bookmarks, and the contents of the Bookmarks folder underneath.
basically: