I have an Intel NUC where 10 Gbps devices can run faster when plugged into the 3.1 Gen 2 ports than the Thunderbolt 3 ports under NVMe load, due to the former having dedicated PCIe lanes and the latter sharing the PCH lanes with the M.2 slots, which could be highly relevant if I were doing heavy disk I/O over a 10 Gbit Ethernet adapter.

This is more than a mild annoyance in the case of faster Thunderbolt devices like eGPUs, especially since, in addition to the 2 PCIe lanes dedicated to the USB ports and a third dedicated to an SD card slot, an additional five lanes are unused.

IIRC there was a reason at one point that Intel insisted on connecting Thunderbolt controllers through the PCH, but I don't understand why they didn't at least use four lanes for one of the M.2 slots. Sure, they may have had to move the SD card slot due to configuration limitations, but in what world is SD card performance more important than NVMe performance?