If I read that article correctly it seemed to be pointing out that sometimes calories are literally mislabeled. That is - a sandwich from a vendor may be labeled as 400 kcal but actually it turns out it was closer to 500 kcal. Casey Neistat did a special for the NYT a couple of years ago about this very problem [1]. The ArsTechnica article you linked did go into other things - but there's definitely a difficulty in dealing with things where labels say one thing and can be 10-15% wrong pretty easily.

[1]: http://www.nytimes.com/2013/02/13/opinion/calorie-detective....

Funny because eating 2000 calories of a carb rich diet maintains my weight, but eating 3000 calories of a carb poor diet and I lose weight. All calories aren't the same, and your body doesn't use them the same. Why is this still controversial?

Because the much more parsimonious explanation is that you're counting calories incorrectly, instead of a wide body of literature being completely false. Put simply, without very careful weighing of everything you eat and extensive tracking, it's impossible to get an accurate assessment of calories consumed.

Eating a caloric deficit will predictably result in weight loss, but there is some feedback between diet and resting energy expenditure (REE). The macronutrient balance you eat can affect REE.

https://jama.jamanetwork.com/article.aspx?articleid=1199154#...

> Among overweight and obese young adults compared with pre–weight-loss energy expenditure, isocaloric feeding following 10% to 15% weight loss resulted in decreases in REE and TEE that were greatest with the low-fat diet, intermediate with the low–glycemic index diet, and least with the very low-carbohydrate diet.

Because diet can affect REE, you can change your diet isocalorically yet still gain or lose weight. Your particular example seems to be an example of this, but the effect is likely very exaggerated. Differences are on the order of 10%, not 30%.

TL;DR: eating less carbs makes you burn more energy.

Because people won't let go of their heuristics, and also the shame and judgement they put on people for being overweight (most of the time, originating in how people treat themselves when overweight).

if you read the article, it covers instances where foods are mislabelled; the calorie content on the back is not correct.

Regardless of the unit eating less will make you lose weight.