Yeah, we did the same thing, .hol files for NPT, and Helicoil thread both inch and metric, plus those funny European PG threads too. It's necessary if you don't want to watch a thousand warnings come at you in Pro/NC (tool bigger than hole, etc). We also edited the drill sizes down to minimize the total number of tools needed by finding commonality between different tap and clearance drills and picking a compromise tool.
The NPT threads surface is not tapered, unfortunately, but that doesn't really create any problems downstream.
Regards Pete