What about insulin sensitivity and different sources of calories. Surely you aren't suggesting that eating a 1k calories of pure protein, pure carbs or pure fat is the same ? Even proiten/carbs/fat branch and have different effects on the metabolism and are required in different amounts for a balanced diet to achieve some desired effect. What about muscle mass vs fat tissue, they burn calories at different rates and require different kind of food to build.

Calories in/out is just extreme oversimplification that doesn't help in the slightest and causes people to starve themselves needlessly because of bad intuition, also risking their health and ultimately achieving the opposite of the desired effect.