What they are doing that is potentially DANGEROUS is tinkering with the voltage reference values that is supplied to the PWM controller.
Essentially the PWM controller needs a reference voltage internally, against which the output is compared by using a negative feedback to change the duty cycle/frequency (usually just duty cycle). To raise the output voltage, you can reprogram the PWM controller if it supports software programming, or use a different reference voltage. What MSI has done that is despicable is that the voltage reference value for the PWM controller is jacked up to a whopping 8.3 volts under load conditions and startup surge. That chip as per manufacturer's specifications only has a recommended reference voltage of 5 volts, and an ABSOLUTE MAX upper limit of 7 volts. By feeding it 8.3 volts as a voltage reference, the PWM controller will be very shortly lived compared to its normal life span. No amount of cooling will compensate for this, since this reference voltage is not used to derive power, only comparison purposes, so jacking up the voltage does not increase internal heat generation significantly, but does shorten (I'm guessing the Vref is tied to a leg of a transistor or opamp internally) the lifespan of that part, in a non-thermal fashion. This startup surge also reacts with certain computers (mainly PSUs) in such a way as to prevent the card from properly POSTING on startup, and non-specific hard crashes when the GPU clock changes (gaming or otherwise).
To make matters worse, MSI did this in a sneaky way. Instead of tinkering with programming or using a different set of resistors to set the reference value at the TL431 regulator that feeds into the PWM controller, they used an inconspicuous capacitor to isolate the regulator from the ground, which it normally connects to. By isolating it from the ground, the regulator isn't really doing any regulation anymore, and essentially, the resistor divider just before the regulator completely sets the voltage. AND, from an engineering point of view, if you just casually examine the board, it LOOKS as if the capacitor is used to bypass the regulator OUTPUT, which is the NORM to stabilize the regulator. THat's why it is sneaky.
The article talks/speculates about the reasons why MSI (having a long history of successful engineering) would do something like this, and do it in the sneaky way. It has to do with Nvidia's TIGHT restrictions on Kepler vcore adjustments. And just this morning, Nvidia officially slammed the door on EVGA's custom voltage manipulations solution, see:
http://www.techpowerup.com/173110/NVIDIA-Forces-EVGA-to-Pull-EVBot-Support-from-GTX-680-Classified.html