The correct PCIe x16 slot is designed to allow full PCIe lanes to the graphics card. This means that it will run as efficiently as possible because it has more dedicated data lanes to pass information. If you try and run a GPU in a PCIe lane that is x4 you will see a significant drop in performance.
Any Asus X99 board can fully support the GTX 970. The Noctua D15 is a CPU heatsink and doesn't play a part in Motherboard/ GPU compatibility, but yes it should work with the motherboard.