It's up to you how you arrange your Favorites tree.
The whole purpose of the Favorites Bar branch is to be shown on a toolbar. If you aren't using the toolbar, there's no reason to have that branch at all.
Looks like Favorites branches can't be pinned at the moment. We'll put it on the list. Thanks!
Sometimes both could be wanted, or somedays a folder tree and some days a favorites bar.
One solution is to remove the branch and turn it inro another prefs page called Favorites Bar List (which of course would require an additional entry in the Folder Tree Contents). Explaining why there are 2 Favorite Lists is easily done now with the new Prefs Help sections. (i.e. 'There are 2 Favorite Lists because one of them is dynamic and the other is not')