I believe differently.
We don't have a good enough grasp of how nutrients work yet. Why does 100mg of Vitamin C from an orange absorb more effectively than 100mg from a tablet? My husband is bipolar, and we've been researching diet/exercise as a control. Bipolars who take a Vitamin B12 supplement alone are less depressed and more manic. But, if they EAT the B12, then it levels both.
Of course, nutrients are just scratching the surface. High levels of insulin support weight gain (hyperinsulenic hypoglycemics gain weight quickly); low levels support weight loss (untreated diabetics lose weight quickly). Protein and fat do not affect glucose levels, one of the defining factors in insulin, as much as carbohydrates do.
If I eat 1000 calories of pure carbs, I'm giving my body much more glucose than I would be if I ate 1000 calories of fat and protein. When the insulin gets involved, it starts stocking the glucose wherever it can. It's used for immediate needs, then pushed into muscles as glycogen, then, when all other space has run out, it starts storing it away in fat cells.
So...I don't believe the calorie is a calorie is a calorie mantra. I believe in keeping insulin levels as low as possible and forcing my body to derive glucose from protein and fat (very difficult) and use the stores it already has.