Yes. ndc and Gage R&R (except when calculated as % of Tolerance) look at the amount of variation you present to it - not the tolerance. So, if part variation is only .03. it will look at how much resolution you have about .03, not 9. If you to get a good ndc and GR&R, you need resolution to .003.
If you supply you data is will be easier to point out the specifics.
If you supply you data is will be easier to point out the specifics.