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.
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.
Man if I was concerned about sinking the time to make a configuration for the compositor with a bus factor of 1 man-child, and a toxic community; I can’t imagine anybody investing the time to make a compositor is going to want to hitch themselves to that cart.
The compositor is really solid and makes for a great user experience but I’ll be fucked if every word vaxry writes doesn’t make me want to move to sway or niri.