You are both sort of right.....but Taubes is probably more right.
In order for me to give this a proper treatment I would have to have more than 2/3 mins between emails/calls to create a post, but the crux of the issue is calorie in/calorie out is true....but most of the reason people struggle with managing calorie in is that excessive consumption of carbs (especially quick burning high GI carbs) starts a process in your body governed by insulin that produces, IN SOME PEOPLE, a RAVENOUS hunger response leading almost without fail at massive overeating at some point.
Some of what Taubes said about insulin also managing how the body stores energy is also true, but probably in the case of significantly overweight people or those that have been, it's much more about appetite stimulation.
You can know each and every calorie you've ever taken in and expended, but - and I speak from personal experience- when that insulin spikes and carbsanity is induced, you are going to crack at some point and overeat. When you do, it isn't going to be a 500Kcal splurge. In my case I could go off for 2K Kcals easily, maybe 3,000, but I happen to be a very large man.
The good news is this is totally manageable through diet without resorting to insanely restrictive eating (though insanely retsrictive modes will work for obvious reasons)....gluten has nothing to do with anything, though by restricting gluten many people coincidentally severely limit their intake of simple carbs( and carbs in genera) which explains why gluten diets DO WORK for some people quite dramatically.
Some people don't have this response or it's muted- that's cool, be thankful.
Some of those people still become overweight, mainly as they age and maintain a typical American sedentary diet. For those people calorie in calorie out and some more activity might work like a charm, but please, do not presume to think that is true of other people because it was true for yourself. We simply have a lot of variability in our individual genetic makeup.
I could bench press 300lbs at 16 yrs of age after like 9 months from when I first touched a barbell seriously. I did BFS Special person programing (3x10 once a week) and had no clue wtf I was doing. That is the product of genetics, not hard work/superior training or anything like that.
Likewise, out response to simple carbs can vary a ton too.
I hope that makes some semblance of sense.....probably not, but I gotta beat this traffic...