Don't think you can do this operation with multiple shapes in one step, whether on one or multiple layers. If you do (i.e., select all shapes in a stack on one layer or across multiple layers) then all objects above will subtract from the bottom shape and result in a single compound object with the fill of the bottom shape. It's as if you first combined all the shapes above into a single object, then subtracted it from the bottom object. At least that's what happens here.
So you first copy the object that you want to use as the "cutter." Now select both the cutting shape and just one of the objects below, then subtract. Now paste in front the cutting shape, select both this copy and just one more shape from a lower layer, then subtract. Then paste in front again, and so on.
Eight pancakes would mean eight executions of the command to see a portion of the plate in the shape of the cutting object.
Maybe someone will be along to correct my understanding of this command and/or to offer a more elegant and efficient way.