The point of the study, from what I can tell, was to show that calories+macronutrients+exercise, the three main current targets of anti-obesity intervention, fa

The point of the study, from what I can tell, was to show that calories+macronutrients+exercise, the three main current targets of anti-obesity intervention, fail to account for a large portion of observed population-scale changes. They aren't arguing generally against total energy balance being involved, only that those three quantities don't constitute a sufficient measure of total energy balance. The implication would be that there are likely other sources of variation, e.g. changes in digestion, metabolism, etc. (the study doesn't really go out on a limb and speculate on that part).