Clearing a layer is the same regardless of the layer type. When an entire layer (not just the front or alpha) is selected for clearing, the front input is set to be cleared by default. You must specify which input of the layer you want to clear by selecting its proxy.
You cannot clear more than one layer at a time. If you select two layers to clear and then select the Clear button, the front input of the first layer you selected will be cleared.
The act of clearing only clears strokes for the current frame. It does not clear the incoming front and alpha of an external layer.
(a) Clear Layer button (b) Selected layer to clear