Using the t2linux guide, Ubuntu kernel 5.13.15-t2-j-bigsur, the USB ports (and audio device, card reader, ethernet port) don't work on a Caldigit TS3.
Video (displayport) works fine.
The Thunderbolt device is authorized (verified via boltctl)
There is simply nothing reported in dmesg regarding the new usb controller or anything related to that.
The answer here turned out to be that I had pcie_ports=compat on my kernel boot parameters.
This prevented any downstream pcie (thunderbolt) devices from taking charge and being downstream pcie things.
Removing that argument, running, update-grub, and rebooting allowed all the ports to work. Related: https://unix.stackexchange.com/questions/566886/pcie-ports-compat-why-port-can-be-treat-as-bridges/593152