Technology

Typically no, the top two PCIE x16 slots are normally directly to the CPU, though when both are plugged in they will drop down to both being x8 connectivity.

Any PCIE x4 or X1 are off the chipset, as well as some IO, and any third or fourth x16 slots.

I think the relevant part of my original comment might've been misunderstood -- I'll edit to clarify that but I'm already aware that the 16 "GPU-assigned" lanes are coming directly from the CPU (including when doing 2x8, if the board is designed in this way -- the GPU-assigned lanes aren't what I'm getting at here).

So yes, motherboards typically do implement more IO connectivity than can be used simultaneously, though they will try to avoid disabling USB ports or dropping their speed since regular customers will not understand why.

This doesn't really address what I was getting at though. The OP's point was basically "the reason there isn't more USB is because there's not enough bandwidth - here are the numbers". The missing bandwidth they're mentioning is correct, but the reality is that we already design boards with more ports than bandwidth - hence why it doesn't seem like a great answer despite being a helpful addition to the discussion.