No, I think it's an excellent demonstration that for most people 'calories in' is the primary driver of weight gain.
There's not an epidemic of people getting fat from eating 2,500 kcal per day but which is mostly refined carbs.
Most people who are overweight are eating far more calories than that, usually as sugar or fat. They have problems with portion control, and recognising just how much they are eating.
I'm being careful to say 'most' because as this research shows there's a small number of people who might be affected by other things.
As another poster points out elsewhere in this thread - that's like saying that fuel consumption is the primary cause of auto accidents.
They have problems with portion control, and recognising just how much they are eating.
Nutrition is about far more than calories in. Controlling cravings through controlling the insulin response is enormously important. The types of foods that make up calories is enormously important.
The relatively recent acknowledgement of the role of the insulin response to refined carbohydrates is a major example of how "calories in - calories out = weight gain" is far too simplistic a view.