I'm speculating, but I think it was mostly written that way as a notification to refs that they shouldn't let a player slide on it because they weren't 100% sure that the nut-punching player meant to do it. In short, it's a direction that basically says, "If it's close, call it, even though it leads it an ejection. We want to stop this." But as often happens when you're writing to send a message, they made it overly inclusive, and the phrasing is essentially "guilty until proven innocent" rather than "if you're not sure, call it".
In short, I agree that, as written, it's a dumb rule. And I further agree that, even as written, I don't think this incident should be captured by it. To me, it was clearly accidental. But it's a judgment call, so there's no recourse (except for the coach to get himself thrown out in protest, which he did).