I tried plugging in the Thunderbolt dock only after logging in to Qubes instead of having it plugged in while the machine starts and it actually works a lot better. When I plug it in after I’m logged in to Qubes, it takes a couple of seconds and then all three of my desktop monitors worked, and so did my external mouse and keyboard. I had to plug ethernet directly in to the laptop’s own ethernet port, and that did work.
I did still experience one crash though a few seconds after plugging in the dock so I’m not sure it’s perfectly stable.
Unfortunately the WiFi still is not working and after reading this two year old thread QCNFA765 (wcn6855) WiFi6 controller not working - #9 by Jakob I believe this is the end of the road as I’m facing exactly these symptoms.