How about, trusted peripherals should speak DTLS over their USB/Thunderbolt PHY, and the OS should keep a certificate store for recognizing them?

This sounds like something that creates a chicken-and-egg problem of there not already being any such DTLS-speaking USB devices... but how about if vendors just create a little USB dongle that wraps whatever's plugged into it in "authentication" using DTLS? Ship the dongle with the laptop; tell people that if they want to install a new OS, they have to plug a USB keyboard in through the dongle.