My CMM software doesn't offer an option for measuring total run out. I can check run out of a circular element or a plane to a line based element. I use both of these measurements only when the call out is virtually impossible to measure with an indicator.
Total run out does not seem to be a good method for verify that holes are on the same center. Best is probably true position: Measure 1 hole, set it as the origin, measure the 2nd hole and tolerance it RFS.
Another option, if the holes you are measuring have thick enough walls, is to measure concentricity. Concentricity compares the axes of 2 cylinders, is fairly time consuming, and is frequently improperly applied, as in calling out the OD of a washer to be concentric to the ID.