I have to drop off my rotors to an auto parts store that does rotor turning in house and I wondered when I pickup my rotors and check it's thicker than the minimum thickness from the manufacture should the rotor thickness measurement be the exact same or can there be a difference in one thousandth? If I take a set of rotors to be turned should both finished rotors be of equal thickness? Shouldn't all waves in the rotor be lathed out?
They should be flat, the grooves and waves taken out. The thickness is a function of how worn each one was going in so they do not need to be the same, the brake system adjusts to those differences by design.
That said, I am not sure exactly which type of damage you are talking about related to the "waves", but if you have a warp in the rotor I would not have it turned even if they claim they can machine the warp out. It will never really balance and will have more issues related to uneven heating while in use.