Great point. I'll pile on by adding that the equations tell you a guideline for BMR, but not a guideline for how to change bodycomp.
The equations completely ignore the role of sleep, stress hormones, and environment on critical factors like insulin sensitivity.
Creating an imbalance thermodynamically (calories in vs. out) is a more important factor in people who are sedentary. Setting aside the issue of food quality, the more you create an anabolic millieu (sleep, micronutrients, hard training, metcon, etc.) the less your body comp will have to do with thermodynamics.
I know you aren't saying this, but to take the calorie deficit model to an extreme, if fat loss was primarily thermodynamics, people could eat donuts and bacon up to their BMR, and spend half the day in an ice bath, and get lean.
Through experimentation (and good notes) I learned that I get leaner when I eat fewer carbs (total calories doesn't seem to matter as much). However, that only happens if I am training hard enough, but not doing too much, where all the stress markers creep up. And the diet and training combo only works if my personal and professional life are relatively stable (long days are ok, but a crisis at work or at home always halts the leaning progress). Training and nutrition, crisis-free, only works when I am free of illness, injury, and pathogens. (For example, when the cottonwoods bloom here, I back off on the fat loss goals. I just try to maintain while I am in uber-histamine-land).
As an aside, I think part of the reason AAS work is that they can bypass these factors and keep the body anabolic.