It's a disconnect that's not unique to the families NG interviewed. Take the Pima native Americans in 1905, where the women, who were quite physically active, basically treated like beasts of burden, had a distressingly high obesity rate, though these families were given a limited ration from the government, mostly white flour and sugar, and not more than 2000 calories per person per day. You can find the same trend in 1928 with Sioux on a South Dakota Crow Creek Reservation--very high levels of obesity in coincidence with extreme poverty. In the early 1960s, MIT nutritionists calculated that Trinidadians were getting no more than 2000 calories per day, yet they were seeing an extreme obesity problem among the females.

Your (calories in = calories stored + calories used) basis for judging other human beings fails because these are not independent variables. Metabolic rate is not constant. If you feed your body few calories, your metabolism adjusts so as to use fewer calories and store more. If you skip some meals, your metabolism is receiving a signal that it had better use the absolute minimum and store the rest to be used in future food crises.

A high-carbohydrate meal causes insulin to be released, and insulin causes sugars in the bloodstream to be stored as fat. And then your blood sugar is low, and you're hungry again. Have you ever noticed the intense hunger that follows an hour or two after a carb binge?

Fat cells that are stimulated to grow (by insulin) scream loud for their share of the energy, just as a growing child's appetite is caused by hormonal messaging for growth and not the other way around. Fat cells scream loud, ensuring that they get their needs met even if the rest of you is weak, tired, and resorting to stealing energy from muscle, the brain, and other tissues. Also, preservatives, additives, and high-sodium foods can cause a person to retain water, which can add to weight independent of caloric intake.

In an older discussion on this issue, travisp shared this article:
http://jama.jamanetwork.com/article.aspx?articleid=1199154
>Effects of Dietary Composition on Energy Expenditure During Weight-Loss Maintenance
>The results of our study challenge the notion that a calorie is a calorie from a metabolic perspective. During isocaloric feeding following weight loss, REE was 67 kcal/d higher with the very low-carbohydrate diet compared with the low-fat diet. TEE differed by approximately 300 kcal/d between these 2 diets, an effect corresponding with the amount of energy typically expended in 1 hour of moderate-intensity physical activity
>In conclusion, our study demonstrates that commonly consumed diets can affect metabolism and components of the metabolic syndrome in markedly different ways during weight-loss maintenance, independent of energy content. The low-fat diet produced changes in energy expenditure and serum leptin42- 44 that would predict weight regain. In addition, this conventionally recommended diet had unfavorable effects on most of the metabolic syndrome components studied herein. In contrast, the very low-carbohydrate diet had the most beneficial effects on energy expenditure and several metabolic syndrome components, but this restrictive regimen may increase cortisol excretion and CRP.

If you consider yourself a scientifically-minded, follow-the-research type, it's time to re-evaluate your (calories in = calories stored + calories used) hypothesis.