Huh? Wherever did I claim that we burn calories unaffected by metabolic physiology? This statement of yours is simply more evidence that you're in way over your head here. You seem to be impressed with the fact that amino acids, glucose and fats all utilize different pathways when being metabolized, and that the efficiencies will not be the same for all of those processes. It's pretty basic stuff, really. So, yes, the burning of calories is absolutely impacted by metabolic physiology. Duh.
If you really understood the subject like you want us to believe you do, you'd realize, like I do, that a calorie is a measure of the amount of energy and that it is always the same no matter what. Good grief, man, that's how a calorie is defined.
Personally, I think you're clenched so tightly, that all those calories you consume spend an inordinate amount of time in your system, and that absolutely none of them pass out of your "pucker hole" unused. You wouldn't have to be so reliant on laxatives and enemas if you could just stop being so freaking uptight.