Runout sets a limit on how out-of-round the shaft at each place along the shaft can be relative to the datum even if the shaft is perfectly round; if its axis is offset from the datum axis it will have runout. Runout does not control the size of the shaft. Neither does it control taper or other shapes - just how much variation there is in the radius to the datum at each place. Total runout does control taper as it controls the variation in radius to the datum for the entire surface.

Concentricity sets a limit on how non-symmetrical the shaft is relative to the datum axis. If the shaft is oval it can still be concentric. It controls mass balance about the datum axis by enforcing diametrical symmetry. It does not control the size of the shaft, or the taper of the shaft. It compares the radius on one side of the shaft to the radius on the opposite side of the shaft at the same axial point along the datum axis.

Position sets a volume the shaft surface must stay in or the volume the axis of the shaft must stay in. The volume the shaft surface must stay in is based on the largest allowable diameter of the shaft plus the position tolerance. The volume the axis must stay in is the position tolerance plus any MMC tolerance allowance. The surface method is the recommended one. Either method should give very similar results for a real part. Mathematically, they are identical.