Stoney

The article says warpage is not common, not that it doesn't happen.

I've written about this extensively, so see my links page, brake section. Bottom line: the Audi HP2 brake rotors are inadequate in their cooling. This causes them to warp prematurely. Sure, properly-designed brakes shouldn't warp. Ours do, I believe....

One can demonstrate that it is probably warpage as I have done: If you have the symptom of pulsation on hot brakes, all you have to do is slow from 70 to zero, speed up to 50 quickly, then brake. It pulsates immediately, sometimes violently. Now repeat: 70 to zero, then up to 50... but wait for a couple of minutes, and then brake. Little pulsation.
The only difference was that they had time to cool off.

I don't see any way that the above results can be produced by transfer of material from pad to rotor and vice versa.

Warpage due to heat is a very common thing in assemblies containing parts of different materials, or of the same material but whose pieces were processed differently such that internal stresses are locked in or thermal expansion rates are different. Heat cycling can also alter the thermal expansion rates of materials... I've done this on certain products I've developed.

On replacement of my front rotors (and rear) for the second time, I used the break-in procedure that StopTech describes. It simply heat cycles the brakes to greater and greater temperatures, which reduces internal stresses and makes them resistant to warping, as well as bedding the new pads.