If you go with a NVIDIA card, you accept the risk that nVidia has been trying to force anyone who uses PCI Passthrough with something other than a $1K Quattro is violating their TOS. They have numerous things they have put in their Windows drivers to make it not work (for instance, you can't tell windows to use any of the HyperV extensions that optimize Windows in a VM). What they do in the future is unknown, but combined with Windows 10's mandatory updates, you may not be able to control what that is or when it will affect you.
A little headache to avoid that and get better performance with AMD was, for me, worth it.
EDIT: AMD is contributing to a completely open source driver which is now in the mainline Linux kernel tree (the AMDGPU driver). Due to this, I would not expect such hi-jinks in the future from AMD. Heck, perhaps they will even get the AMDGPU driver to gracefully release from the host for use in the VM in the future!