This particular article doesn't try to tell you "X good, Y bad", it's saying eat less, exercise more, or more specifically, if you want weight loss, as long as your diet leads to a caloric deficit, it doesn't matter _what_ you eat.
I should have been broader: I'm saying a simple narrative can't possibly tell the whole story of such complex chemical processes, whether it fits that particular snoclone or not, which includes "a calorie is a calorie". It's a leaky abstraction.