disc brake rotors are design with this kind of thing in mind - to skim.
that is why we can see that disc rotors have relatively thick surface. whenever machining is done to resurface (skimming), usually its less than 1mm deep. the person who do it will find what is lowest point on the uneven surface then only they will start the process. i can assure you it is less than 1mm every time they do it. unless it is too bad where they will recommend you to replace the discs at all.