This Noctua fan is too thick so I ordered a Cooljag BUF-A4 and an Evercool EC6010TH12BP fan. The fan is PWM, 60mm and 10mm thick which would be great. The Cooljag heatsink is thinner than the Supermicro SNK-C0054A4L so I should get at least 5mm free on top of the heatsink + fan. Airflow should be better than now.
Supermicro fans: "57" v"54" - you probably should have gotten the "57".
A 40mm noctua was about the same thickness as the fans in the image above (10mm thick maybe??)
Noctua just came out with some 40mm PWMs i thought - been a while since i looked.