I (despite the article) am mostly in agreement with you, but I think that calories out is a very complex subject. For example, when I calculated how many calories I was burning on my longer runs, it ended up being around 3000 calories/week. However, as I said before, my intake went up. Way up. I ate like an idiot. Donuts? Yeah. Cheeseburgers? Sometimes ordered two. Dr. Pepper? Bring the two liter! I absolutely added more than 3000 calories to my diet after I started running. And yet despite all that, I just kept dropping weight.

The human body is a very complex, non-linear thing. Discerning operating principles by looking solely at inputs and outputs is a hard problem.