> You should be measuring the ATP yielded by eating food.

The closest practical approximation of this is the calorie measurement we assign to foods. Sure our metabolic processes are not equivalent to a calorimeter - but its easier to measure calories than to account for the specific metabolic process each gram of macronutrient you consume goes through.

So for all practical purposes, and in the context of hormonal effects, energy in vs energy out ie CICO is still law.