That is simply stunning! I don't understand how the physics even could work here...the rotors were depleted at the same (or greater) rate than the pads??? (assuming these are the original pads). I had the new low-dust pads put on mine (per the TSB) at 20,000mi. No mention from the dealer then about skinny rotors.
I would ask for your actual rotor thickness measurements from the dealer and the factory new measurement versus the min thickness requirement.
I have actually been LIED to by my dealership's service manager on more than one occasion. I have every reason to distrust this service department. Now when I have to use them, I make sure everything is documented.
I think you can get rotors for about $100 each, pads for about $50 front, $50 rear. So for $500 parts, leaves $250 service. That's about par for Lexus. I would question new rotors in the rear especially. The whole thing is preposterous.