Your sources don't support what you're saying. The fact that our bodies use more calories to burn specific types of calories is irrelevant to the contention that 1 calorie=1 calorie. Comparing one calorie of protein to one calorie of carbohydrates and they are the same as far as energy content goes. The fact that one is harder to digest isn't relevant to their actual baselevel energy content.
Actually, they support exactly what I'm saying. Look, if you eat 1 calorie and by the time it's reached a usable state in your body, it's got the energy value of .97 calories and another calorie in that state has the energy value of .77 calories, and you've exercised to where you're burned .77 calories, then the first calorie will result in stored energy, the second will not. That's why 1 calorie does NOT always equal 1 calorie.