I don't really think it proves anything about "calories in calories out" the way most people mean it.
For most of my life, I thought all calories were equal when it came to weight loss. I assumed I would lose just as much on 1500 calories of junk as 1500 calories of whole foods. I never tested the theory, so it took me nearly 40 years to understand just how much it mattered where the calories came from.
If I drastically cut calories (regardless of where the calories come from) I do lose weight - but I don't have to cut calories nearly as drastically if I choose carefully where the foods come from.
I can eat more and feel better when I keep carb-levels fairly low. No doubt part of the equation is having more energy to burn more calories without even realizing it.
Another huge factor is hunger. On 4000 calories of high-carb foods, I am far hungrier than I am on 1000 or low-carb calories. Appetite and hunger control can be powerful tools for weight loss.
It all does boil down to calories in/calories out, but it's more difficult to determine the calories out than the calories in. It's also difficult to determine how the calories in affect the calories out. Metabolism is a bit like a fire - the fuel you use not only affects how long the fire burns, but how hot the fire gets.
I can see that literally in my body temperature. It's not unusual for my body temperature to be in the low 96's. I used to think I just had a naturally low body temperature. Then I discovered that when I'm eating a relatively high-carb diet, my body temperature is at least a full degree lower than when I'm eating low-carb. The fewer carbs I eat, the closer my body temperature is to "normal." It's also just a study of one, so I can't conclude anything for anyone but myself, but to me it proves that "a calorie is a calorie" is an oversimplification. What you eat can affect what you burn.