The changes were so simple that I laughed at my own over-analyzed solution and bought unnecessary replacement accessory parts. Since the noise was caused by the high speed fan at 4000 RPM, the best way was just to replace it with fan of lower RPM.
Two major issues I faced. First, is very hard to get a cheap PWM 4 pins 92mm fan in MY unless you bought it together with the heatsink or your source it from Taobao. Second, you can reuse the existing 6 pins JWT A2504 connector instead of buying a new one. Even so, I can't get the exact model but similar 6 pins 2510 connector works just fine.
In the end of the day, I've learned so much about casing and heatsink fan and their related power connector. Such knowledge should be quite handy in case I need to build another workstation in coming future.
Result before and after replacement.
$ sudo apt-get install freeipmi-tools lm-sensors
Default server fans
$ sudo /usr/sbin/ipmi-sensors | grep Fan 1344 | REAR FAN | Fan | 4000.00 | RPM | 'OK' 1408 | CPU FAN | Fan | 4000.00 | RPM | 'OK'
After replacement with lower RPM fans.
$ sudo /usr/sbin/ipmi-sensors | grep Fan 1344 | REAR FAN | Fan | 1803.07 | RPM | 'OK' 1408 | CPU FAN | Fan | 2241.20 | RPM | 'OK'
I forgot to capture the result before the replacement but I recall it should be the same, roughly around 35C to 39C.
$ sudo sensors-detect $ watch -n 1 -d sensors coretemp-isa-0000 Adapter: ISA adapter Core 0: +37.0°C (high = +83.0°C, crit = +99.0°C) Core 1: +36.0°C (high = +83.0°C, crit = +99.0°C) Core 2: +38.0°C (high = +83.0°C, crit = +99.0°C) Core 3: +35.0°C (high = +83.0°C, crit = +99.0°C)