You should thoroughly steel brush the flat hub surface against which the rotor mounts. If you do this, you shouldn't have to worry about runout.

The easiest way to do this is after removing the bearings and seal from the hub for cleaning before repacking, clean the hub to get all the old grease out and then dry. After drying, take it to the steel brush on the bench grinder and clean the flat surface THOROUGHLY until it shines.

If you don't have a bench grinder, use a handheld steel brush, or a steel brush on a drill motor. After this step, rewash the hub internals to ensure that you have not left any steel brush fibers in there to spoil your wheel bearings.

Good luck,