Isn't it already well understood by now that energy storage is controlled by hormones and _what_ we eat directly influences the presence and quantity of those hormones circulating through our bodies?

As long as insulin levels are kept in check, energy storage is as well. Avoiding sweets and simple carbs while having plenty of fiber in your diet is an effective means of achieving that. It's not necessarily calorie restricted, calories are somewhat orthogonal.

There's a story Gary Taubes tells about Oskar Minkowski's [1] discovery of the Pancreas' role in insulin production. I found it quite illuminating when trying to better understand nutrition and will paraphrase it here. The guy was experimenting with dogs and removed the pancreas from some dogs, buttoning them back up and letting them continue to live normally. He observed they lived normal lives as if nothing changed, but no matter how much food they ate - they kept losing weight. They would eventually die from the weight loss. He had noticed that flies were attracted to the urine of the pancreas-free dogs, and being a scientist, he tasted the urine and observed it was exceptionally sweet. Not having insulin in the blood, this stuff just came out in the urine rather than being stored in the fat, because fat cells need to be instructed to steal excess energy and store it, otherwise it just passes through.

Hence if there are foods we can eat which cause the pancreas to behave anomalously for extended periods, our energy storage will follow suit.

There's another story Taubes tells, I think these were from Good Calorie, Bad Calorie but I've read so many things on the topic it's a blur. It's about a woman who had a small tumor removed from her brain, the tumor was next to I believe it was the Pituitary gland. After the succcessful removal, she began gaining weight uncontrollably. Her diet/lifestyle was unchanged from before the surgery, and no matter what they did to her diet to try fix this, she gained more weight, eventually becoming obese. It turned out a part of the brain affected by the surgery controlled the hormones related to energy storage. This woman's body was internally starving itself by erroneously instructing the fat to continuously store energy. If memory serves this story had a good ending though, they discovered a medication to get the hormone production back to normal levels and her weight normalized.

These two anecdotes are important. Any engineering-minded person who has done troubleshooting of comple systems, root-causing of difficult problems, understands the tremendous value in observing how systems fail.

The stories demonstrate a total decoupling of Caloric intake/physical activity to energy storage. Stop fixating on calories, we need to eat foods that keep the energy system functioning properly in the first place.

I don't think it's surprising that we find the more a diet is composed of intact, naturally-occurring foods, having little processing/preparation (including cooking), the more health tends to generally improve. Unless you're steeped in religious beliefs to the contrary, you probably understand and accept humans evolved over a long period of time. Our bodies are still suited to the foods we evolved around, so when we eat things like refined carbohydrates, stuff that requires machinations and technology to create, we're exposing the body to essentially unexpected inputs. So we should at least expect bad results to be more likely when consuming such things.