Probably I just don't get it, but I don't exactly understand what's the problem here. In the bottom screenshot, should the UI elements be transparent, without the white area above? You need to set the frame of the UIView in your UIViewController appropriately and I guess you might have to set the background color transparent:
self.view.backgroundColor = [UIColor clearColor];
I'm not sure, since I never use the IB, but it may be possible to set the Alpha value of the background color of the base view to 0. Not the alpha of the view itself, but of the background color.