matalik,
When you say "bore", are you talking about the tap drill?
As the designer, drafter and inspector, you have no interest whatsoever in the tap drill. Don't specify it. Don't apply tolerances to it. Don't inspect it.
Machinists know, probably much better than you do, what size drill to use prior to tapping. If your machinists need you to tell them this, this might be the source of your problem.
For a tapped hole, specify the size, the pitch or TPI, the tolerance class, the depth, and the positional tolerance. Add a perpedularity specification to the tolerance box if you need it. Buy thread gauges to inspect it.
If your bore has some functionality other than allowing you to tap a hole, then you apply the tolerances needed to meet that functionality.
JHG