Isn’t this glossing over that (when allocating 16 PCIe lanes to a GPU as per your example), most of the remaining I/O connectivity comes from the chipset, not directly from the CPU itself?

There’ll still be bandwidth limitations, of course, as you’ll only be able to max out the bandwidth of the link (which in this case is 4x PCIe 4.0 lanes), but this implies that it’s not only okay but normal to implement designs that don’t support maximum theoretical bandwidth being used by all available ports and so we don’t need to allocate PCIe lanes <-> USB ports as stringently as your example calculations require.

Note to other readers (I assume OP already knows): PCIe lane bandwidth doubles/halves when going up/down one generation respectively. So 4x PCIe 4.0 lanes are equivalent in maximum bandwidth to 2x PCIe 5.0 lanes, or 8x PCIe 3.0 lanes.

edit: clarified what I meant about the 16 “GPU-assigned” lanes.