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I'm guessing that the fans are controlled by the PMU. The PMU runs independent of the main CPU, and I'm guessing that this approach is easier than having the PMU talk to the drives through the SATA controller, requiring drivers, OS support so that the OS SATA driver and PMU doesn't interfere with each other etc.

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Correct. However in this case it's the SMC managing it. PMU comes from the PPC era, like CUDA in the clone and 68K times.

SMC handles all low level monitoring, because it's OS independent reading data via SMART is just a non option. SMC also takes care of how hardware components are initialised and a slew of other things. See > http://support.apple.com/kb/ht3964

Secondly, while you can override certain SMC values like fan speeds you can never override the lowest safe values that are hard coded in. In that same vein if the SMC thinks your fan should run faster when you don't want them to, they will regardless.

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