The article draws up comparison to defining "wealthy" as "People get rich because they take in more money than they spend." but that's actually a perfectly fine definition of wealthy which explains what it is. Similarly "is an energy imbalance between calories consumed and calories expended" is a fantastic definition of obesity. What the article actually argues against is again the idea the primary causes of imbalance are portion sizes, advertising, culture, abundance, and so on rather processed foods and quality of diet changing the way the body processes and measures energy intake from food.
I agree heavily with the latter part but the it is still describing a consumption/expenditure balance issue. This research isn't replacing that rather trying to find more ways to combat the issue that may not be explored as much previously.
The other thing is intake reduction still works it's just much harder than it may need to be without a proper diet. The article quotes "To attribute obesity to “overeating” is as meaningful as to account for alcoholism by ascribing it to “overdrinking.”" as if that means alcoholism isn't an intake problem. It is, but the best way to fight the intake problem may not be just saying "drink less" and that's the type of thinking actually being proposed in the research.