I've had pad transfer vibrations with my OEM brakes/pads (all OEM) and tracked it plenty when I lived in Europe with it. After Nurburgring weekends I would notice the pad transfer grinding/vibration issue for a while and after about 300miles or so under normal driving the uneven pad material would wear away with no vibration. My current AP BBK has vibes and I and a tech are working through it and it's probebly pad transfer issue like with the OEM brakes, but I've never tracked it since I put the AP kit on.
So with that I never experianced warping rotors, OEM or AP's. But pad transfer being uneven does cause alot of vibrations. Also OP, you mentioned you don't have progressive braking, that the braking feels hard and causes the car to jerk when stopping which could be a leading cause to something else happening.
I think take the advise from one of the other reply's here and revert back to OEM, wheels, pads, everything again for a while. Go to another dealer and have them address the jerky braking feeling and go from there.
Did you get to see the measurements taken with a dial indicator that the BMW tech probebly used to see if the rotors were over .003" of run out? Normally rotor disc run out can be up to .003" and you should not feel any vibrations below that value, assuming there is no uneven pad transfer materail on the disc surface.
Also if not checked already, have the tech measure the run out of the hub bearing. If that were an issue, it probebly would translate into an unbalanced feeling in the wheel(s)/steering wheel but I wonder if its just slight enought to cause eventual vibrations in the brakes. Just an idea to not leave any stone unturned.