This idea of calorie intake and expenditure being an epiphenomenon... Taubes certainly does say things that seem to suggest that, but what it would even mean for that to be true?

Calorie intake and expenditure are automatically regulated by the body, and in a healthy person, marginal increases or decreases in calorie intake will cause matching changes to both appetite and to energy expenditure, by changing body temperature, fidgeting, and other expendable metabolic processes. Large, forced decreases in calorie intake must cause either a balancing release of energy from fat cells, or a matching reduction in energy expenditure, but unfortunately, it's likely to be the latter. In that case, the energy expenditure comes from sacrificing metabolic processes that aren't really expendable, damaging health. Obesity can only occur if this regulatory process is broken somehow. It is more likely to be broken by a high-carbohydrate diet than by a high-fat diet. If it's broken in someone who's on a low-fat, high-carbohydrate diet, then switching to a high-fat low-carbohydrate diet is likely to fix it.

The previous paragraph is what I believe to be true. I don't know how well it lines up with what Taubes has said, but I don't care because Taubes is just a human. It does seem that he's failed to communicate it clearly, but if you're going to criticize him for that, the criticism should be delivered in the context of a clear restatement of the same position. If you're going to go around saying things that are incompatible with the previous, then please address it directly; everything you've said so far is at least one step removed, and it's frustrating because you keep saying things that aren't even wrong.