I was the AC above and I did actually read your reply. I agree with your thermodynamics approach, if you'll grant me that the actual equation is:
A*(cal in)-B*(cal out) = C*3500lbs
Where A, B, and C are efficiency factors that depend on physical processes occurring inside the machine that is a person (yep, I'm agreeing with you about the mechanical idea)
When I was training, no I didn't track what I ate very closely. Why would I? I was working out 25 or so hours a week. However there have been times in my life where I tracked my intake obsessively. We can forget the first 10ish lbs, they're easy. But beyond that I seem to lose weight somewhere around 17-1800 kcal/day with an hour of exercise. That's not very much food. A friend decided to try to lose 10 lbs along with me, she weighed 135 and barely worked out. Her baseline food intake was approximately 2500 kcal. 1700 was starvation for her.
And that's pretty much my argument. We can control the height of people with food intake too. If you don't eat enough as a child, you will not be as tall as you would be otherwise, however when someone is very tall or very short we don't blame them for it. Yes, put me in a concentration camp and I'll lose weight. But the question is, why is it so difficult for some people and for others, they just never had to worry about it?
One more interesting data point, in at least 1 followup study for weight loss (I don't have the source right now) formerly fat people had to eat approximately 1/3 less than people who had always been at that weight in order to maintain. That's giant. It's the difference between 3000kcal and 2000kcal. At 2000kcal, you have to be pretty careful about what you eat. At 3000kcal, you really don't need to be careful at all - as long as you aren't eating an entire onion bloom at chili's every day, you probably won't gain weight.
Many people in this comments section keep pointing to one thing or another thing as a pro or a con. But there are a ton of factors, everything from brown fat to gut bacteria, to genetics as well as food availability and type, medication usage, and the overused "glandular (thyroid) problem." (Don't get me started on thyroid problems, they are not very common - genetics is a far easier argument.) And we really can't point to any single factor as THE REASON. However what we can say is that there are a variety of human responses to food, exercise and energy storage and therefore an equation like cal in - cal out = 3500 x lbs may be off in some people by a factor of two. One way to think about this is that auto efficiency has changed dramatically in my lifetime, even though power output has been increasing. It's possible to have two mechanical objects that are very similar in form and function, but that have very different inputs and outputs. And I'm sure you'll agree with me that cars are bound by the laws of thermodynamics.
(There's a study I've looked for in the past and never found, but it's incredibly obvious... I'd like to monitor people's intake and then measure the calorie content of their poo. I'd be willing to bet that skinny people poop out far more calorie rich poo than fat people.)