The top comment there pretty much nails it.
Actually, it's an advantage. Have you tried to use the menu on monitor 1 when the app is on monitor 3 of your Mac?
http://blog.boastr.net/?page_id=79
But his other points that Unitys "wonky" auto-hiding of the menubar is misguided UI seem reasonable to me.
Do we still hear people complaining the window buttons moved to the right?
The top comment there pretty much nails it.