Ok, this is embarrassing, confusing, frustrating and enlightening, all at the same time:
It turns out my judgement was being clouded by the noise the Seagate Ironwolf disks were making. So I had the impression the Noctua fans were doing a lot of noise. They simply weren't.
I turned off the FreeNAS, letting only ESXi run (FreeNAS is a VM on my machine). The machine was virtually silent, and I could basically hear only the case fans, which are not loud at all.
I then opened the case, and reinstalled the original Supermicro fan. I put on a very lower speed, and it was still audible, though bearable, and the CPU was way cooler with it, even at a lower speed. The "PUE2 (Power Utilization Effectiveness) Speed" mode works beautifully with the Supermicro fan. At the same rpm, I feel the Supermicro fan/cooler gets the CPU at least 5-7 degrees cooler. When I put the machine down on the basement in a few months, when I get proper cable there, I will surely put this fan back.
I reopened the machine, put the Noctua fan back, as the machine is staying in my living room and I do want the least possible noise, and rearranged the hard disks, such as not all of them are on the same cage. I got three hard disks there, one Barracuda and two Seagate Ironwolf. The temps are now drastically lower. I'm not even sure I'll put more fans on the machine. During a scrub, the HDD's were about 35-37 ºC. So I guess airflow was an issue here. I also am waiting for some bracket adaptors from Fractal Design, as their cage doesn't support 4-screw hard disks, so the disks are not super stable.
I guess my next upgrade - which will wait a bit - will be more silent disks. I'm not referring to the spinning, as it's quite inaudible. It's their standby noise that is a bit too loud.
Sorry if I annoyed you guys with a non-issue. I believe the Noctua fan can be a good addition if you don't mind the CPU not getting as cool as possible (ie., low 40's, upper 30's ºC, but rather 52-54 C), and the Supermicro cooler is not as bad as we might think, depending on your environment.