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i agree with you that there IS a tolerance to consider
....but you're saying that the few thousandths is a bigger margin of error than grinding something by hand??!!!
anyway....
You could chuck it up and not indicate it and it could be out .010", or it could be .003", who knows. If I was going to use a lathe, I would stick an indicator to it to see what I was dealing with before I made the first pass.
Say it was out .010", then yes, I can keep it closer than that by hand.