Only months later I came upon a solution in a comment on the QubesOS github page.
It turns out vBIOS was not the problem at all. The drivers for the GPU kept failing because on the GeGorce 50 series there is some conflict where the vga adapter will fail if you pass it together with the audio part. Yes, despite being in the same IOMMU group and against the usual recommendations on these cards passthrough works only with graphical part used alone. When I detached NVIDIA HD Audio Controller from the VM everything magically started working on both Windows and Linux based qubes.
Another important lesson from that github comment is that to check if the configuration is working you must restart the VM with the attached GPU twice. That is start it, shutdown it, and then start it again. Otherwise you will get false failures on valid setups. That can be a source of endless frustration.
Posting this for everyone who struggles like me with the NVIDIA GeForce 50 series.
TLDR if you have nVidia GeForce 50 series card:
- only pass through the graphic adapter device from your GPU
- restart the VM twice when changing configurations to avoid false failures