For a spotface, material is removed from a surface to make it flat and smooth, usually for a fastener or a bearing.
By comparison, a countersink makes a conical hole and is used to seat a flathead screw.
Standards exist for the sizes of counterbores, especially for fastener head seating areas.
The pilot matters little when running the cutter in a milling setup where rigidity is assured and hole center location is already achieved via X-Y positioning.
The lower counterbore is designed to fit into a drill chuck, and being smaller, is economical to make as one piece.