Sorry for goofed up grammar in previous post.
A few things about the "Myth..." article:
1. In the article, the word "runout" is used. "Runout" which is greater after the rotor has been used than when the rotor was in the box is what we're calling "warp" on this forum.
2. Warping is the dimensional change of the rotor. There are three basic ways this can happen. Heat (causing expansion, cooling causing contraction, not always in nice ways), stress/strain, material added to the rotor (from the pads, presumably). The picture shown to illustrate the latter (material deposition on the surface of the rotor) shows patchy spots of pad deposits. The only way deposits could appear that way is due to localized dimensional variation (loss of flatness in this case) and/or localized superheating of the rotor (which coincides with loss of flatness--heat-related dimensional changes again). I have also seen pictures of rotors with deposits which were consistent all the way around the friction surface. They were from racing projects. I can't think of anyone I know who has had any type of pad deposits on their passenger car or truck rotors. I am not denying it could happen with some rotor and pad combinations on someone's vehicle, just that it's universal.
3. The article completely ignores the effects of braking forces on the disk itself. It's complicated, and I would want to run FEA simulations and tests to fully understand the effects (perhaps they are thinking of racing hardware, which may differ greatly from on-road applications). As the iron rotor gets hot, it wants to succumb more to the massive squeezing and pulling forces coming from the calipers and pads. One effect of a long, severe stop with a bargain-basement passenger car rotor made of low grade iron would be the slight "spreading" or "stretching out" of the friction surface, some of which might stick around after the event is over. What's left is a friction surface that has a few thousanths of "wiggle" and thickness variation, maybe only enough for 1-3 variations per rotation.
4. One effect of the "squeezing and pulling" could be stress relieving, in the case of rotors made from lower-grade gray iron castings. It's conceivable that rotors turned from castings that were too small to begin with (not enough material cut away from the raw casting) would leave rotor surfaces with inconsitant microstructures which would behave differently when subjected to heat and stress.
5. Warped brake rotors aren't a myth. Lots of rotors warp. Mine have warped in the past. I know lots of people who have experienced warped rotors, and I have driven their cars and observed the effect. On one of my own vehicles, the warped rotor caused the steering weel to twitch at very low speed. I removed the rotors. While removing them I observed perfectly clean, bright gray iron. I also saw that when I spun them on the hub, they rubbed the pads the way my bike rims used to rub my brake pads after I crashed into a curb!
The following is an excellent resource for understanding passenger brake rotors in depth--pages 60-88 are probably most useful:
http://www.sae.org/events/bce/tutorial-ihm.pdf
K