The shooter is not going to have to defend himself in court. The bad guy will be charged with at least breaking and entering, if not assault. The matter is settled by the police decision not to charge the shooter.
If they charged him, then it would be a matter of determining whether or not it was a justified shooting. Because he's not being charged, there is no question as to whether it was or not. Any discussion re:the shooter is, ultimately, moot, because he doesn't need to defend himself in court.
BTW, I do read your postulate with an open mind and I understand (I think) where you're coming from with it, which is why I didn't say it doesn't apply here. We might, however, disagree whether or not the bad guy was armed.
IMO, the question as to whether or not the bad guy was armed here was, again, answered by police. It was assault, and they were satisfied that the shooter was in fear for his safety.