Even on desktop motherboards, the space under a M.2 slot is usually nearly empty. On laptop motherboards, it is almost always completely empty save for possibly a thermal pad. Some laptops position the M.2 slot to have the SSD extend beyond the edge of the motherboard. But in either case, laptops are not reducing PCB footprint by using M.2 SSDs, because nothing gets stacked under the SSD; that space is reserved for the SSD.