Modern motherboards often don't have PCIe slots next to the x16 "GPU" slots, as they'd nearly always be under the cooler, so why waste PCIe lanes (and BOM cost)

Modern motherboards often don't have PCIe slots next to the x16 "GPU" slots, as they'd nearly always be under the cooler, so why waste PCIe lanes (and BOM cost) on a slot there? The increasing trend towards x3 and x4 width cards might mean you'd be able to use the next but one slot (assuming they don't get removed soon...), but even then there isn't really standardisation about what type of PCIe slot goes (or doesn't get fitted) in which position on the motherboard.