Adding this in case anyone else has the same question in the future:
The NH-U14S TR4 heatsink in my Gigabyte X399 Aorus Xtreme prevents installation of a graphics card in the top PCI-E x16 slot unless the 3 mm or 6 mm offsets in the heatsink’s mounting brackets are used to shift the heatsink away from the slot. The amount of shift needed will depend on whether or not the graphics card has a backplate and, if so, its thickness.
Another solution is to mount the graphics card in a lower slot or to use a vertical graphics card mount, like the one that came with my Fractal Design Define R6. With a vertical mounting bracket, the NH-U14S TR4 does not need to be shifted because the PCI-E ribbon cable is so low and narrow that there is no interference with the heatsink.