Saying that the human body is significantly different from a 'heat engine' is just common sense, too.
Yeah. My experience has been that energy balance - calories in vs. calories out - is a critical element to weight loss. But the composition of that energy balance - macronutrient breakdown of the calories in, how you burn the calories out - determines what body comp you end up with.
So if you cut to 1400 kcals a day and do cardio and eat high-carb, low-protein, you'll lose weight, but a good chunk will be muscle. If you cut to 1400 kcals a day and do weight training and intervals and eat high-protein, low-carb, you'll lose weight and most of that chunk will be body fat. In my experience, anyway.
Both are important - if you just worry about CI/CO, you're missing half of the picture. If you only worry about macronutrients and not quantity, you're still missing half the picture. The workouts are more self-evident, I think - if you build muscle while you train, you'll burn more energy. If you do too much aerobic/low-strength workouts you'll encourage your body to cut back on the "unneeded" muscle to return more quickly to homeostasis.
This is all IMO and IME. YMMV. ETC. :)
For my part, when I biked a lot and ate a low-calorie diet (and only cared about calories), I lost a lot of weight and all my lifts went down, too. When I switched to low-carb, lower-calories, my body fat went down but my lifts didn't. When I switched to low-carb, eat all I could eat of protein and fat, my weight went up and my lifts didn't. Now, well, all hail carb cycling! :)