Our body functions predominantly on ATP, not on glucose or fructose or fat or protein. ATP gets generated from those other macromolecules in pretty complicated

Our body functions predominantly on ATP, not on glucose or fructose or fat or protein. ATP gets generated from those other macromolecules in pretty complicated biochemistry. You're definitely right that thermodynamics governs everything, but it governs it at the ATP level and not at the macronutrient level. Those additional layers of abstraction distort the whole calories in-calories out math. Eating the "right" thing is more important than eating the "right" number. Consider eating 800 calories of protein versus 800 calories of alcohol (also technically a macronutrient). You're going to metabolize each differently, and you'll probably feel better eating the former than the latter. This is obviously an extreme example, but the point is that things that you eat affect your body in ways beyond that magic calorie number.