I may be confusing a few things together, especially with server NICs. TOE support is pretty handy for reducing CPU usage by moving a few calculations out of the network drivers and onboard the NIC. USB vs PCIe, I was under the (possibly false) impression that USB was a polling only protocol, at least for USB1 and 2. That, and doing some searches, it looks like some faulty USB drivers in some Windows versions were leading to higher then normal CPU usage for audio and NIC devices, something I ran into with my old CarPC setup.

Offered the choice between two similar priced products, I do believe a Thunderbolt (PCIe) NIC would still be the better choice over a USB one. Especially when the USB choice is USB2.