UPDATE - Solution
It looks like AGESA AMD BIOS version 1.0.0.4 Patch B (1004 B) fixes the Nvidia pass-through D3 errors for folks with x470 and x370 Ryzen AMD motherboards. This patch was introduced in late November 2019 to AMD motherboards. Mobos confirmed working after updating to this BIOS version:
* Asus Prime X470 Pro + 3900x
* MSI B450 Gaming AC
* MSI x470 Gaming M7 AC + 2700x
* X370 Taichi + ryzen 3900x
* Gigabyte AX-370
* Asus x470-F with 2700x and 39
Wanted to follow-up. The cause for my issue [with the Ryzen 3900x hanging while trying to pass-through USB Controller 3.0] was totally that FLR issue posted above. Luckily, someone on this forum had already compiled a kernel with a temporary fix, and I used that. Find that custom kernel for Unraid 6.8.3 here:
Note that I tried Unraid 6.9.0-beta1 and it did not yet have the FLR fix in the Linux kernel. It will eventually make it into the Linux Kernel, but probabaly not until 5.