Rotor replacement

I own a AAMCO 4000 drum /rotor lathe. It has been my experience that if the run out on your rotors is .005 or more you more than likely going to feel brake pulsation. When I turn a rotor, the best results I have been able to attain on my lathe is .001. Which is more than good enough.
So I would assume that if there's an issue with runout you would turn the rotors after they were attached to the hub? Together as one unit?