Thunderbolt controllers in BIOS-assisted enumeration mode go to sleep when not in use.
All that is left is a PCI hotplug bridge with no child bridges attached.
The Thunderbolt controllers that break this rule are:
- Titan Ridge
- Presumably any future controllers released after Titan Ridge
- Some Alpine Ridge controllers with updated firmware and BIOS to support (uncommon)
From the above link, we find a command to force the power and wake the controller (usually used for firmware updates without requiring Thunderbolt devices to be attached).
"echo 1 | sudo tee /sys/bus/wmi/devices/86CCFD48-205E-4A77-9C48-2021CBEDE341/force_power" without the quotes, should wake it up. Then "lspci -vnnt" to visualise the difference. If you want, you can post the output of "lspci -vnnt" for us to confirm for you.
But this only works on recent kernels. I cannot remember which one was the first, but 4.20 most definitely has it (and definitely some earlier ones but for the sake of simplicity, just use that one).
Hopefully this works and allows for your Thunderbolt controller to be acknowledged by Ubuntu. However, since you said you do not have any Thunderbolt devices, I am not sure why you care (although I do not say that discouragingly). But that should be the solution.
Oh, and remember, if you have another Thunderbolt 3 laptop and a USB-C to USB-C cable with USB 3.X speeds, you should be able to connect the two laptops together via their Thunderbolt ports, which will wake the controllers and result in emulated 10GbE networking in between them. If they are both Linux then you will have to "sudo modprobe thunderbolt-net" on one of them.