You really think vfio-pci never send commands to the card?
If it is the case, how linux can put this device to sleep? Vfio-pci manage the card. It just pass command from vm to the card :)
I know, i have ~5 pcie controllers linked to my vm, gpu, nvme disk, usb controller, audio controller and sata controller.
nvme and sata controller can navigate between linux and windows without problems, drivers seems pretty stables.
USB controller, and gpu can't be used on linux if they are not "cleanly" shutted down by windows. (usb controller can't execute commands, and my r9 290 hard freezes)
PCIe reset is really complicated because it work differently on a pcie device to another.
I tried during a period to dompmsuspend vm then host. And re-start vm at host wakeup. Sometimes it work, sometimes hard freeze.
Think that this capacity was never tested by AMD and nvidia. Just because it never happen in real life with 99.99999% of computers.