I don't see why not, airflow is airflow, and I usually have no problem connecting noctua fans to a supermicro motherboard.but I am not sure if it is a good idea to change it. But the fan is attached just by screws, I could probably remove it and replace it by something more quiet?
It's the case fans I usually have problems replacing with noctua, the SM motherboards tend to cycle through high then low mode. I know it is fixable by playing around with a script on the BMC, I just prefer to connect the fans to a separate physical fan controller.
On windows you can also set the max cpu usage in the power options. There must be something similar in linux based OS. That's another way to ensure it doesn't go all the way in term of TDP even under load.
Not a bad idea to log the temperature of your different components (MB/CPU is accessible via ipmitools, HBA via storcli, disks via smartctl), so you can measure the long term impact of what you do.
Also lots of people add an additional fan pointed at the PCIe cards: HBA, 10gbe NIC and AIC SSDs will benefit from it. It allows to make up for less airflow from powerful case fans if you replace them with quieter fans.