Firstly, I was a brake system Engineer for a global OEM, working with Bosch, Ate/Continental, Ferodo, Brembo, Akebono, Fagor Ederlan etc. All brake materials have to transfer onto the disc and is part of the bedding in process. It's the temporary bonding between the transfer and the pad that produces some of the braking force at lower speeds and braking forces. Under heavier braking, any abrasives in the material will actually remove some of the transfer layer and allow a fresh layer to develop.
What will produce a disc thickness variation is runout of the disc surface when fitted. Your brake pads
will move back from the disc when you stop braking, which is controlled by the brake seal. If the disc runout is close to this, then the outer pad will lightly rub the disc surface, which slowly wears this section of disc down. Eventually this will be felt as a pulsing of the brakes and pulling on the steering. The runout can be due to the disc manufacture, but also the hub. The hub must be cleaned of any surface rust, debris etc, and then check the runout with the disc clamped correctly. I used an old wheel cut down to just the centre and then tightened and torqued the wheel / lug nuts.
I have run standard road car brakes until they are glowing bright red in abuse test and not once did I warp a disc as long as you drive it gently until the brakes had cooled down to more normal temperatures. (Easy when you have thermocouples and IR temperature sensors fitted).