Is there any way to set mating tolerances so that if the bolt circle diameter of one set of holes (e.g. clearance holes on a flange) isn't exact with the bolt circle diameter of a set of tapped holes, the mate command will still work? The reason I ask is often the manufacturers model will use 3 digit precision (e.g. 10.312) while our part has 4 digit (10.3125) and I can't mate the parts together and clock them appropriately.
I don't think so. You will probably need to have only one concentric mate, and use something else, such as Parallel, for the other one.