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.
This is the first post from you with which I agree.
You said that well.