My understanding is that the Calories in each bit of food are intended to be "the amount of energy you absorb" (on average, I guess? in the same way that averages are used for how many you burn when exercising). So a better synonym than "energy" for Calories as used in nutrition might be "usable energy" (excluding the energy content of the food that you poo out).

Yes. And the efficiency of "food calories - shit calories" varies wildly between individuals and across time for individuals. The number of calories you see in a food database is calculated based on how well a few macronutrients literally burn in a lab setting. All it tells us is a way to compare input values, not usage or output.

Feces is composed of material your body could not break down into usable nutrients, combined with materials your body is attempting to excrete.

Combined with approximately 50% by mass of bacteria.