Here is my 2 cents.
True Calories in and True Calories out is really a function of what you are eating. not the amount you are eating.
What does your body actually do with the calories you put into your mouth?
If I were to eat pure sugar all day my body would digest it all and through a long chain of reactions convert it to energy and fat stored in my body. If I were to eat fat and protein all day by body would digest some of it for energy and pass on much of it.
So regardless of the EXACT amount of calories you put into your mouth there is some variation as to how much your body actually takes out of your digestive system.
Calories out: (ignoring exercise).
All humans burn some amount of calories just living. If I am using carbs as my predominant fuel source then my body will burn 1000 calories over the course of a day just by living, regardless of the amount of carbs I take in. If I am using fat and protein as my primary fuel source my body will burn 2000 calories over the course of a day just by living.
If you I don't get enough fat/protein my body thinks it is starving and therefore lowers my metabolic rate and stores calories as fat. If I am getting enough or extra fat/protein my body is not worried about starvation and therefore burns at a higher metabolic rate and is not concerned with storing calories as fat.