Good point, it looks like the Supermicro heatsink may be a little more efficient, plus it’s a tad less expensive and more compact. Was there a second image in your post? I’m just seeing a red X next the Epyc die diagram.The NH-D9 DX-3647 appears to concentrate the heat pipes longitudinally at the midline. The Epyc 7002 chiplet layout puts the chiplets out toward the package edges. So, the heat piples aren't where you want them to be. The Supermicro HSF heatpipes appear to be perpendicular to the long axis and would seem better suited for the Epyc 7002 chiplet layout. Looking forward to seeing some pictures!
EDIT: Well, if you look at this picture the chiplets are not at the edges so the Noctua option wouldn't be terrible except that each heatpipe is going to cross 4 chiplets and the i/o die but the Supermicro configuration would put each heat pipe across just 2 chiplets and the i/o die would get a heatpipe of its own.