The thickness of the anodized coating is accounted for in the blueprints for both the lower and the parts themselves. If you follow the ordnance prints for hole sizes, and properly drill and ream them, and the anodizer follows the spec for the coating, then the thickness of the coating is already taken into account.
Even if the anodizer exceeds the spec for coating thickness (which is seldomly the case as thickness takes time to grow, which equals $$$) it isn't an issue. Worst case, where the layer is too thick, lube the part well, and using fine sandpaper, lightly sand the interior of the hole. You're talking dimensions on the order of 0.001" or less, so sand very gently. It will remove a little anodization and allow the part to fit.
If you go the professional route, I doubt you'll run into this. Although Mil-spec calls for a minimum of 2mil thickness (0.002" or 50.8microns), part of the definition of Type-III is that it be thicker than 25.4 microns (anything greater than 1mil). Every commercial (i.e. non-military) AR upper/lower I've run into and measured (colt, bushy, rra) have all met this definition of being slightly more than 1mil thick, but none have even come close to being 2mil thick. You shouldn't have a problem with dimensions, but if you do, its easy to resolve.