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I've read somewhere that it is possible to use USB3 port to debug physical devices. Has anyone tried it? How does it work? Are all controllers capable of doing it? Is it possible to use it on PCIe based controller card? Is entire USB stack required to use it?

The EHCI and xHCI each are capable of, and might include a debug port and socket. Not all cards include this feature. You must check the PCI(e) Vendor and Device IDs to see if that particular card supports the debug feature.

Then, if found, there are certain techniques to use the debug feature, each described in the specification.

P.S.: You can also determine if a controller has the debug capabilities via the xHCI Extended Capability chain.
P.P.S.: If you don't know much about the USB, the xHCI Debug feature will be a considerable venture. :-)

Ben
- https://www.fysnet.net/the_universal_serial_bus.htm