I am assuming you are referring to the rear flanges that were original meant for the drums. I didn't even measure mine, I just took the stub axles off and sent them to the machine shop to have machined. I figured Arizona Z knew what they were doing , so I didn't question it. I don't think much had to come off and I haven't had any issues.
Measuring .003 out of flat on the flange will mean that further out on a 12" rotor -it will be worse. It's a PITA , but you probably need to do it.