Where the confusion comes from is that PWM is indeed used to control the speed of DC motors. But PC fan motors aren't really DC motors, they're actually small 3 phase synchronous motors with built in inverters to let them operate from DC. The inverter's PWM input merely emulates the operation of a DC motor and controller. The DSP that drives the inverter in Delta fans does a lot of advanced computation to synthesize the sine waves (using its own PWM!) that drive the motor, which might as well be called "Cindy Wu black magic".
But let's abstract that out. We supply the fan with 12V and give it a PWM signal. Increase the duty cycle of the PWM signal and the motor runs faster. Decrease the duty cycle and it runs slower. You can use an Arduino to generate that PWM signal.
Now let's try using the Arduino to sense the incoming PWM from the motherboard. Connect a 4k7 resistor from 5V to PWM, then connect a 10k resistor from PWM to an Arduino analog input. Also connect a 10uF capacitor from the analog input to ground. Now just get an analog voltage reading and it will be proportional to the incoming PWM duty cycle.
Then put the two together with whatever mapping (input vs. output curve) you want and there you have it!

in this way looks like more understandable for my ignorant ears, even if in the first part after a while the discussion starts to become more and more gobbledygook (I don't know if it's the best word to express it as English is not my mothertongue, but what I mean is: WTH is a Cindy Wu black magic?)
anyway, the discussion is very interesting and deserves more time, but sadly at the moment I can't afford to spend time (to study Arduino,I really need it to barely understand something) and money (I know Arduino is designed to be cheap, but if I start dealing with it I won't be happy until I'll have
all the accessories that I might need, even stuff I'll use like once or twice in my life!), so I'll move towards the direction of fan replacement/tricking the the system check:
I suspect it's gonna be enough if I just cut the wires of the fans' plugs and make an adapter 5pin->3pin classic, and after I use a simple controller to drive any fan I want...
but this is something I'll do on my next day off, as today has ended up differently: infact this morning I've finally got delivered my 4 new (just to say)
E7450 hexacore 


so I've spent almost the whole day playing with a 4 for the price of one (literally)
35kgs build 
right now I've just finished to test everything and I'm fuxxxxnly happy to see that this 300£ power hungry coffin scores almost
1400 with cinebench r15!

I know it's nothing too special, but for me it's a great result, as Cinema 4D is one of the software I use, and until now I couldn't go above the 850 of my o.c.ed 4770K..I mean, I've never seen so many buckets in a system of mine! ...this is giving me the idea to make a nice and detailed benchmarked thread, comparing properly this two systems, as when I was planning to buy the server HP i got almost crazy because I couldn't find any useful benchmark about the e7330 (or e7450)...I put it in the list of the things to do
edit:added a couple of pictures, soon I'll edit the first post adding detailed pictures of the fans and relative circuitry, temps with occt, and I'll organize it with a summary of the potential solutions for the noise/heat problem
sorry for the long post and some OT