Nope. The auto pilot is a module you slot in, end of gameplay. If an NPC pilot just means hiring and of you go, I'm also opposed to that.
If however the NPC has adequate gameplay involved, that makes all the difference. Want a skillful pilot pilotting your ship, that pilot will charge you proportionally. But good pilots are also a rare commodity, so some crew statistics like loyalty, chemistry with other on board NPCs need to be taken into account. Probably not a good idea to have a Federation pilot and an Imperial gunner in the same boat. Longer serving NPCs loyalty will increase over time. You could also hire a cheap rookie and invest time in training him so you'll end up with a cheap loyal pilot. Stuff like that.
I don't see the possibilities in gameplay with regard to an auto pilot.
And I answered you because you asked.

Other people just state: it's the same thing.