We don't get it from raw bomb calorimetry ("Burn it and measure how hot it gets"). There are additional absorption coefficients applied before the nutrition label is printed. But for proteins, fats, and simple carbohydrates the coefficients are quite high (~95%), while progressively more complex carbs have a declining curve that ends in indigestible fiber. The difficulty is that the same person will digest more or less of the protein in their hamburger depending on how many fries they ate, how greasy those fries were, whether they ate lunch, and how much beer they drank that night. It's variable.

We might know the inner workings of the "machine" but we can control inputs (food) and measure outputs (weight).

Let's say I eat 3 hamburgers per day and gain ~1kg per month.

If I reduce that to 2 hamburgers per day I maintain my weight.

And when I reduce that to 1 hamburger per day I lose ~1kg per month.

That is simple. As for how I feel while eating 1 hamburger that's another question.

I can try to improve the machinery of my body by e.g exercising, eating healthier food, adjusting my macros, taking supplements, etc.

So now I can eat 1.5 hamburgers per day and I feel better and still lose 1kg per month.

While this is strictly true - measurement of calories gives the upper bound of possible energy absorption. This makes it sufficient to calculate if TotalCaloriesIn >= TotalCaloriesOut. Obviously there are some biological complexities - but within the boundaries of the system the outcomes are constrained by the laws of thermodynamics.

"We measure food's calories by burning it" - are you sure that how it is done?

Humans (unlike say cows) do not digest parts of what is available in plants, which makes some vegetables filling and ultra-low caloric.

"we don't really know how many calories a given person will get from eating a given piece of food"

exact numbers of unknown, but difference is not so great, except truly extreme cases (and vast majority of fat people is not fat due to them)

add to that food calorie labels arent required to be 100% accurate, there's an acceptable range like +/- 20% iirc. That's enough to throw off a precise deficit. Calorie counting is more about directionally helping you lower your food consumption but it isnt as accurate as people think.

Honestly the main thing was learning that perfectly satisfying food I cook at home tends to land around 600-800 cal for a meal, where eating out almost anywhere is often twice that, even if my beverage is water. Just being aware how how heavy those otherwise delightful meals are gives me pause. Granted these figures are all a side effect of my personal eating habits and preferences, but that's rather the point of the exercise isn't it? There's a lot of individual variation, and the individual is probably best served by a personalized approach.

Eating out, especially in the US, is horrifying when you look at serving calories.

Why does every major restaurant feature individual meals with a caloric intake of an entire day’s energy?

If I'm smart, I can offset this by eating half of that meal in the restaurant and taking the rest in a to-go container. Two meals for the price of one, and reheating in the oven is almost as convenient.

Separately though, I have no idea why restaurants seem to exclusively offer gigantic portions over here. I wonder how common this is elsewhere in the world? I'm not well traveled so I genuinely have no idea.

Presumably the recommended daily calorie intake figures (and the calculators for these) do to some extent take this into account? i.e. I would imagine they're based on experimentally tested values rather than theoretical energy expenditure.