That's what they're doing on iOS7 also.
One of the questions floating around for the past few months was whether the next OSX would go in a flatter direction, and if so how they would cue window overlaps. It looks like the answers are (a) yes and (b) using roughly the same shadowing as before, plus translucence.
Both the Notification Center and the Control center on iOS "overlap" the screen through translucency. It could be argued that the parallax feature is also another attempt at differentiating layers within iOS, coupled with some of the animations i.e opening folders (also translucent), and multitasking.
That being said, I feel that iOS is unable to convey relationship of layers/overlapping windows well the way we are all accustomed to with desktop computers.