It’s also about metabolism and what you eat does impact your metabolism. Not all calories are the same.
A calorie is a measure of the amount of energy and it is always the same. It has always been defined in this manner. Amino acids, carbohydrates and fats are all metabolized using different pathways, and yes, there will be different efficiencies for each. There is a difference, however, between a calorie, and the efficiencies of that calorie.