If we study this in a quantitative method that can prove causation that Calories cause people to be fatter, and we will likely see a general imprint that everybody is not different. Yet, there will be variation, so how do we explain the variation?
That is why these more qualitative studies are useful.
I have studied digestion, and I can say in general, the principles should be universal. But, how do I explain an anomaly like that more African blacks tend to be lacto intolerant vs Europeans? A qualitative study can show that certain people lack the enzymes to breakdown the milk sugars etc. You have to dissect people individual to come up with the evidence.
This drums up another point I made earlier, if person A ate 6000 Calories and person B ate 3000, and they had the same daily routine, who would be fatter?
You can't answer that without more information because the Calories in person A's diet may be mostly cellulose, or things that are not digested due to the lack of bacteria's and enzymes needed to break the diet down.
Therefore, a person who eats 6000 calories of, mostly, salad daily vs a person who eats 3000 that has a slice of cake in there, person B will likely be fatter. Calories are not digested equally, nor are they used equally. Counting them may help you in general, but understanding the qualities of food and your own body will be better if you want total control.