add a box in the tool definition for a tap in order to account for the tap's lead-in. this could be used with the drill tip through bottom checkbox in the tapping toolpath.
eg/ a 4-40 spiral flute machine tap has a 0.045" lead-in, such that a hole tapped .25" deep will only have .205" of full threads. adding the 0.045" into the tool definition would eliminate the need to calculate the actual required depth to tap to for every tapping toolpath.