What I mean is that "calories in" is not literally calculated by the total energy you put in your mouth, but rather the energy your body absorbs from that. And as you note that might be different based on the food, how the food is prepared, content of the food, etc.

Likewise "calories out" is not literally calculated by adding up your movement & exercise. We know that things like hormonal levels, etc can all impact how much energy your body is expending.