I think I have already acknowledged the biochemical feedbacks - I've been very careful to talk about food digested rather than food eaten, and did also mention some of what the body can do to regulate itself. But in the absence of a calorimeter able to take readings from the gut and bowel, or the willingess to measure the calorific value of food excreted or egested, or indeed the ability to measure accurately energy converted from stored-in-food to kinetic or heat, the crude estimates of food eaten and exercise taken will have to do.
You simply can't ignore the laws of physics. You can acknowledge that psychology, biology and biochemistry are important (and I think I have) in determining weight gain and weight loss, but physics is always at the heart.
I think in the broad scheme of things you're correct. You certainly can't change the laws of physics, something IIRC Atkins tried to do. And it's important to talk about food that's digested rather than eaten as under different circumstances our digestion will absorb nutrients differently. However it's still a calories in/out at the end of the day, I can't see there is any other way around this.
I think it get's fuzzier when we take into account our bodies response to certain foods or eating patterns - the feeling of satiety for example can have a profound effect on our desire to eat - our food choices however can influence this and certain 'diets' possibly work in that way.
There is also the effect of constantly being surrounded by foods(one of my biggest issues!) or the smell of foods which trigger hunger cravings. Add-in the food choices we make, the increased role of eating in social situations and a bizziliion other lifestyle factors it's no surprise that intake control is difficult.
The key to losing weight unfortunately is more a mental challenge than simply a physical one. It's about adjusting lifestyles, eating habits, refusal,self control. Fad/Diets are simply a prop for exerting some kind of control in an acceptable way.