The claim being made is that somehow, due to the cooling - locally, and not uniformly around the periphery of the rotor (due to getting the brakes hot then stopping and not moving, with brakes continuing to be applied) the metallurgy has been changed... so much so that turning them on the lathe results in either the cutting of the bit being non-uniform (i.e. the rotor remaining thicker [once machined] where the material is harder [this is a bit unlikely, though]) or the rotor being harder locally and then subsequent rotor wear is less at the harder areas and accordingly the brake action pulses. Doesn't happen immediately though.
Essentially the cast iron rotor(s) are being heat treated. Actually, the grey cast iron, being quenched... the faster-cooled areas of the rotor being converted to martensite (I think). Actually, it may be that the area under the brakepads might be cooling slower than the rest of the periphery of the rotor... or if it's wet, rainy, it may be that the area under the pads is being cooled much slower than the rest of the rotor periphery...
Martensite is hard... but to be honest I don't know if it is steel that is heated to a certain temp then quenched converts to martensite... or if grey cast iron does this. (My engineering metallurgy course was ~ 45 years ago, hehe).
SO, in these circumstances, the only solution is rotor replacement.
Interesting side note... The first car I drove, learned to drive on, had for a good while after too... a '70 Oldsmobile Cutlass, had 9" dia frt brakes, drum brakes. Absolutely inadequate for the car... (which had a Rocket 350 4 bbl, 310 gross HP...). BUT... that car had absolutely smooth brakes, no pulsing... fade, yes, but no pulsing, no vibration.