I've never had a dog become a slave or drone with positive reinforcement. That's the nice thing about it, is they learn that they can control what happens to them through their choices. My dog REALLY wants to chase that rabbit, but he knows it is a better choice to ignore it and stay on the trail with me.
There is probably something to be said for the over confidence of puppies, but generally you want your puppy to have a good experience with EVERYTHING. When I ran across an aggressive dog on the hiking trail when my pup was 4 months old, I wasn't worrying that he wasn't scared of the barking dog, I was treating and playing games and engaging him as the dog passed by.
And positive reinforcement does not change their instinct. My dog has plenty of instinct to chase down and maul small furry things. His reaction to them is controlled because I have conditioned him to have immense amounts of self-control when faced with a stimulus like that, but all of that instinct to chase and kill is DEFINITELY there!