Here is where there seems to be a disconnect. I'm 100% behind you concerning the boldened statement. In fact, now that TN is a Castle Doctrine state the law is more on your side now too.
What you don't seem to understand in regards to the incident you mentioned is that in the circumstances you describe you basically jettisoned all your legal protections under any aspect of "self defense". In fact, if some prosecuter wanted to really make an issue of it, you'd be having to defend yourself for unlawful carry (I'm under the impression you don't have a permit, I could be wrong) for running around outside your home with a loaded gun and if you pointed the gun even remotely at the guy assault.
You simply must grasp that once the guy took off you have ZERO argument for self defense. If you run him down you have now instigated the confrontation. If you shot him, even in the leg, you'd be in court over it. If you had killed him you'd be screwed.
Look, I'm not arguing the morality, practicality, or even sanity of how the laws are set up. I'm also not offering you an opinion. In the incident you described if you had shot the guy the legal system would have chewed you up. And again, that's not even addressing a civil suit. Some dirtbag wants to break into your house at 2:00 AM? Ventilate him with my blessing. Run around with a gun and threaten lethal force against an unarmed person who tried to flee the scene? Just...don't.