I disagree on it being a bug for holes. You would not drill a 1" diameter hole to put a 1"-8 thread on it. So the bottom hole diameter will be the diameter of the #'d bit used to drill the hole.
In this case for internal threads - a bit for threading a 1"-8 hole will NOT be 1" in diameter. Its a 7/8" hole.
So you can't have a bottom of hole thats 1" in diameter AND then cut 1"-8 threads on it. The bottom of an untapped hole will be the minimum diameter. Even with a partially threaded hole you still will drill out the diameter for the desired % of threads.
Shafts is likely because its one body and i agree that is super annoying.
Ryan Bales
Fusion 360 Product Support