It would seem pretty straightforward and intuitive that people get the same amount of calories from identical foods.
However, that is not true.
Once food enters our bodies -- especially our colon, it encounters our microbiomes. Everybody has a different microbiome -- little bugs/bacteria in our gut. Some of these bacteria convert undigestable foods into usable calories that are then absorbed by our bodies. (Short Chain Fatty Acids.) The amount of food converted by these bacteria varies depending on an individual's unique microbiome.
So, it turns out that no, not all food results in the same amount of calorie absorption. This is something that varies significantly, and not just based on the microbiome, though this is certainly one of the factors.
Let's say you and me eat the same food. I get 2x the calories out of the food as you do due to my super gut biosphere.
Therefore, if I want to weigh the same, I must eat half the food.
Your argument is an argument for why Calories are not perfect, and I 100% agree.
However, you can just pick any calorie amount as as starting number. Weigh yourself on a scale ever day. If weight is going up, decrease calories by 200 per day. If weight is going down, increase by 200 per day.
The exact rate of burning calories is not important. And that is why the 2,000 calorie a day diet is a very very rough guess.
You're assuming that the body absorbs calories the same way, even under different circumstances, such as various caloric intakes. This isn't always true.
People too often assume that bodies are like cars, and that food is like gasoline. This is not true. Our bodies are far more complex (and interesting) than mechanical machines. The food we eat is also far more complex (and interesting) than gasoline as well.
Calories in == calories out. Right. Calories in is diet, yes. Calories out is influenced heavily by hereditary and lifestyle factors that are outside of diet.
However, that is not true.
Once food enters our bodies -- especially our colon, it encounters our microbiomes. Everybody has a different microbiome -- little bugs/bacteria in our gut. Some of these bacteria convert undigestable foods into usable calories that are then absorbed by our bodies. (Short Chain Fatty Acids.) The amount of food converted by these bacteria varies depending on an individual's unique microbiome.
So, it turns out that no, not all food results in the same amount of calorie absorption. This is something that varies significantly, and not just based on the microbiome, though this is certainly one of the factors.