I agree, can't imagine a rotor warping from a bicycle in the same sense that a rotor on a car would do from heat, wear and rapidly being cooled by hitting a puddle of water. The rotor surfaces might have been uneven like you indicate from the factory and improperly machined when manufactured ? Perhaps unevenly torqued when assembled ?

Anyway, maybe your cable is adjusted to clamp down on the rotor too tightly and need to readjusted, unless they are hydraulic ? That seems to be something I do even with the older style brake pads, my adjustments are for minimal travel to squeeze on the rims. Perhaps the sliders need to be greased so they travel more freely and release. Pads might be unevenly worn. Thank God I avoid high maintenance and more complex systems on bicycles. I don't think I'll ever own a shock absorbing fork or full suspension bike, simply because I don't want to ever replace something that I feel should last a lifetime as rigid fork and hardtail.