To be fair to Taubes, his research is relatively old -- meaning 1999 to 2006. In low-carb terms, that's a generation ago. I don't expect him to be correct in our entire metabolic makeup, and it certainly isn't intentional. IMO it was enough for him to disprove Ancel Keys. Cut the man some slack.
This "calorie is a calorie" stuff is nonsense. Feeding somebody carbs is like putting a 2.5 gallon can of gas in the back seat of an electric car. Sure, it's energy, but the car isn't going to burn the gas. When the car runs out of electricity, it doesn't "see" the gas can. It asks for more electricity.
Of course, this is a very simplified version. Our bodies have the genes to burn carbs and fat. If you want to burn fat, you have to convert from a carb-burner to a fat burner, mainly by ditching carbs altogether. Once you do that, only THEN does your body see the fat and burn it (with a calorie deficit, of course).
5'0" female, 45 years old. Started Primal October 31, 2011, at a skinny fat 111.5 lbs. Low weight: 99.5 lb on a fast. Gained back to 115(!) on SAD chocolate, potato chips, and stress. Currently 111.