The stencil is not used at the moment (well... that's actually how overdraw debugging is implemented) because the hardware renderer only support rectangular clipping regions and thus relies on the scissor instead. Given how the original 2D API was designed, using the stencil buffer for clipping could eat up quite a bit of bandwidth or require a rather complex implementation.
It is planned to start using the stencil buffer to support non-rectangular clipping regions but this will have a cost.
Remember that the GPU rendering pipeline was written for an API that was never designed to run on the GPU and some obvious optimizations applied to traditional rendering engines do not necessarily apply.