The maximum allowable front disc brake rotor runout is specified to be 0.003 inches ON VEHICLE. This is the combined hub runout and rotor runout.
The combined runout may be vastly minimized or even eliminated by reindexing the rotor on the hub. Maximum hub face runout is 0.002 inches.
An on-car lathe can minimize runout by cutting rotors parallel to the direction they rotate. Ford and several other vehicle manufacturers recommend on-car rotor resurfacing for fixing runout problems.
Surface finish can also be critical because it affects the friction characteristics of the brakes.
Lastly, and often overlooked, is the disc brake rotor thickness variation. The maximum allowable thickness variation is specified as 0.0004 inches, less than 1/2 of one thousandth of an inch.