I'm using am an Rampage III Black Edition and it can also switch off the PCIe. So the R3E is the first Asus Board that can do this, just an FYI
On my Black Edition it's the following behavior, iirc (I tested it a long time ago):
If you turn of the PCIe Slot the cooler of the card stops working and the screen goes out, and it did not come back...