I would check the spindle on the inside, right on the taper. If that has no runout it should be ok. Even .0001 is acceptable. You will always find runout on collets when checking with gauge pins. The amount on most collets will be in the tenths range, from .0002 to .0005 depending on the quality of the collet. You will not find perfect in any sense with most machine tooling unless it is laboratory grade, even then it’s subjective. Most of the machine work done in general industry standards is in the tenths range, and most of us in the hobby shop, find we only work to 1/2 thou ! We don’t control the environment in order to work any closer than that.