Brake rotor runout - how much the rotor wobbles side to side as it spins - has to stay within tight limits, or you get a pulsation. Knowing the typical spec helps you understand why a clean install matters. Here is the runout picture.
What runout is
Runout is the lateral (side-to-side) deviation of the rotor face as it rotates - measured with a dial indicator. Even a perfectly flat rotor will show runout if it is mounted on a dirty hub. See brake rotor runout for the basics. It is different from thickness variation, though runout leads to it over time.
Typical acceptable limits
Most vehicles specify a maximum runout of only a few thousandths of an inch - commonly around 0.002 to 0.005 inch (check your service manual for the exact figure). That is a tiny amount, which is why cleanliness and proper mounting are critical - a speck of rust at the hub can exceed the spec.
Why it matters
Excess runout makes the rotor wobble into the pads once per revolution, and over miles that high spot wears thinner, creating thickness variation and a pulsation you feel when braking; see what is brake judder and new rotors vibration. Runout is a leading cause of a "warped rotor" feel.
Keeping runout low
Clean the hub to bare metal before mounting a rotor, torque the lugs evenly in a star pattern, and check runout with a dial indicator if you have a persistent pulse; see clean new rotors before install. A properly-mounted quality rotor stays within spec. Fit rotors with quality pads and fresh hardware.