You don’t absorb 100% of the mass of food into your body. For example; fiber, which tends to be dense and heavy, passes right through and out the back door.
If you want to try to calculate the amount of energy derived from food (which is what calories are), you can only count what gets absorbed, not what gets excreted back out.
Body fat is a way to store that energy. More calories = more energy = more fat required to store that energy
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