Looking at Firefox 4, a new control was added to main-window that is the parent of navigator-toolbox.
tab-view-deck is a deck that contains the controls and it has a vbox inside it that then contains all the toolbars.
The vbox inside tab-view-deck should have an ID associated with it so that CSS can be cleanly applied to the navigator-toolbox:
#main-window > #tab-view-deck > #MISSINGID > #navigator-toolbox
The vbox in tab-view-deck needs an ID so add-on developers can insert overlays in the vbox. For example, the following XUL overlay does not work as desired; it inserts a second vbox after the first one under tab-view-deck:
<toolbox id="my-addon-toolbox" insertafter="browser">
<!-- toolbox contents here -->
I think this bug should be marked FIXED,
bc this was done in Firefox 6 already, it is <vbox id="browser-panel"> now. (I'm using it for xul overlay also)
bug 610996 was the one that fixed it.