In the end, PowerTune 2.0 fixes one of the three variables, temperature. That leaves power and clocks to fluctuate. Since power is fixed by design (or PCIe specs in some cases), clocks are effectively pinned at a given point. This point is essentially overclocked to the maximum possible frequency given the other fixed constraints. AMD says the Hawaii/R9 290 family can modify the clocks on a per-clock basis, good luck topping that with a manual switch. For any given set of temperature and wattage values, without other physical constraints PowerTune 2.0 can extract the maximum possible performance out of a GPU on a clock by clock basis. And now you know how and why.
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http://semiaccurate.com/2013/12/16/amds-powertune-2-0/