As far as I am aware, the only useful application of the food energy hypothesis to practical obesity management are the recommendations that people increase their daily physical activity, do resistance training to build muscle mass (thereby raising resting metabolic rate), and eat specific foods that may increase resting metabolic rate. Notable examples would be caffeinated black coffee and unsweetened tea, which provide nearly zero food energy while the caffeine temporarily boosts metabolism. Compounds found in Capsicum peppers are suspected of temporarily increasing metabolic rate (though the effect diminishes as the body acquires tolerance). The resveratrol in berries and grapes is also suspected of causing white adipose cells to temporarily become "beige", where they mimic brown adipose cells. That third recommendation is, in essence, to take [non-caloric, herbal] drugs to boost metabolism.
As you suggested, the element that makes it useless for practical adiposity management is the fact that human bodies adjust resting metabolic rates, psychological impulses to consume food, and psychological impulses to adjust physical activity levels in response to dietary intake. One person drinks a sweetened beverage and starts bouncing off the walls for the next two hours, burning off that extra energy. Another drinks an identical portion, then becomes lethargic and turns every last sugar molecule into stored lipids. We don't [yet] have a model that can predict a structured diet for a specific person that can reliably produce the desired effect.
The labels on food packages and the calorie counting websites get their numbers from nutritional assays, rather than in vivo measurements in actual humans. The latter would be prohibitively expensive, would produce results that are far less precise, and offer foods suppliers no competitive advantage.
This is why diet plans that don't require calorie counting are relatively popular. People just want to follow a diet where they can consistently lose excess adipose tissue without either literally working their asses off for hours a day, or constantly suppressing the psychological impulse to eat more than is allowed by the plan. Whatever other mechanisms may be in play, some diets work best for some people for just one reason: they can feel satiated and stop eating at a caloric intake level consistent with fat loss, without having to constantly do math during their day.