I've got some good news!
After further testing, I've realized that the original 4-pin fan connector from the PSU does NOT map 1:1 with a regular 4-pin and I actually ended up killing one of my fan because I initially connected thinking it would map 1:1 (the usual black, yellow, green, blue).
The actual mapping is :
black - gnd
yellow - ctrl
brown - pwm
red - power (12v)
After looking through the spec from digi key for a similar fan I came to found out the actual mapping.
https://photos.app.******/S4TMs2GtoNHz9bHu9
I connected a noctua A9-14mm fan to it (with low noise adapter) and it's running super quiet now in IDLE. Even for boot/wake from sleep it's not super loud like before since the max RPM this fan can do is 1700 RPM with the LNA (13.5db vs 41 db from stock fan). The fan 92mm fan fits perfectly atop the PSU, I plan to make a mesh-like aluminum shroud to replace the original vent-less cover.
The fan is only 14mm so it only add a bit of height (14mm), making it a total 52mm or 2inch!
Super stoke that is mod is working.