While you have a point, I think there are plenty of examples where application managed multi-panes are useful.

* Emacs (and other text editors) * IDEs * Terminals * etc...

Man, if I found a browser that gave me expressive enough keyboard shortcuts to make using a mouse optional (like Emacs) I would be switch to it in a heartbeat. Heck, Emacs style pane management and buffer switching might be enough.