Overlapping UIViews with interactive transitions between view controllers have rapidly become the hallmark of a good iOS UI experience. I personally haven't ever seen overlapping UIWindows though...
That's not what he means. The naming of which view or window class we're referring to is meaningless. iOS 7 features the same concept where views slide and transition onto the view you're looking at (which as you pointed out is not new in iOS) using translucency to indicate depth and layering. For example, see notification center, control center, and others. That was a new concept, and it's been brought to OS X now.
