Tolerances are determined by functional requirements then manufacturing processes are selected to cost effectively achieve those tolerances. Even if you already know that you are going to CNC mill something because it's the only machine available today there is no point in specifying tolerances that are smaller the the part needs to function. Unnecessarily tight tolerances increase costs in many ways including additional tool changes, extra inspection, scrapping perfectly good parts, etc.
Just because something is CNC milled does not mean you can always achieve the same positional accuracy. If there are surfaces machined in one chucking with the same tool the result will be much better than if multiple tools are used and the part has to be flipped over and re-chucked.
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The Help for this program was created in Windows Help format, which depends on a feature that isn't included in this version of Windows.