That's what I was thinking but every time I would research a board I would get a different answer. For instance when I researched the Asus Z9PE-D8 on New Egg, the reviews were that they actually did not support high end cards. When I looked up Supermicro boards and spoken to their customer service, they told me that they only use their special made gpu.
Don't equate GeForce GTX 6XX gaming cards with a Quadro 4000.
The customers on Newegg are complaining mostly about the GeForce GTX 690's compatibility with the ASUS Z9PE-D8 WS.
I didn't see any of them complaining about workstation graphics cards.
Two customers used a Quadro 5000 and another used a Quadro 6000 with that motherboard.
It looks like ASUS is still trying to work the resource allocation bugs out of their motherboard's BIOS.
Of course Supermicro will try to get you to buy one of their own cards.