Technically it measures how much you can heat up a known volume of water if you burn the food. We have no way of measuring how much of that energy released by combustion actually gets absorbed and translated to ATP in the body, but it’s the best estimation we have of the relative energy content of foods.

There’s some carbohydrates, proteins, and fats that our bodies don’t seem to convert to energy (or only partially convert) but still technically contain “calories” because they’re combustible. Sugar alcohols, fiber, etc.

Plutonium doesn’t combust, but it would heat up water in a calorimeter. Really the test method’s applicability kind of falls apart when you start testing undigestible materials.