It isn't so much that calories in/out is false, as the equation of "calories eaten - (activity + bmr) = weight change" that is false. The food you eat has a massive impact on your biochemistry (and thus your metabolic rate), and microbial metabolism also varies significantly depending on the substrate you provide them.
The beginning of the article linked says "if you usually consume 2,500 calories a day and then cut back to 1,600 calories, you’re going to lose weight from that 900-calorie daily deficit — even if all you ate was potato chips. But you won’t be healthy and you most likely won’t be able to keep the pounds off."
I went from 245lbs to 185lbs by eating 1500 a day every day for 5 months, that was over a year ago and I still weigh 185lbs, all I did was when I hit my target weight was make sure that over a week my diet averages out to 2500 a day, some days I go over by a few hundred, the next day I just under eat by a few hundred so that it balances out.
