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, 44 years old. Started Primal October 31, 2011, at a skinny fat 111.5 lbs. Low weight: 99.5 lb on a fast. Gained to 109 on sugar cheat. Reset with 85P / 90C / 90F. Currently weaning off fat to 85P / 90C / 60F.
MY PRIMAL: I (try to) follow by-the-book primal as advocated by Mark Sisson, except for whey powder and a bit of cream. I advocate a two-month strict adjustment for newbies. But everybody is different and other need to tweak Primal to their own needs.