Yeah, like someone else said further up, food calories are typically measured in bomb calorimeters but our body isn’t a bomb calorimeter. It might be more accurate to say “calories absorbed/calories burned” since like you noted, the actual energy contained in food doesn’t necessarily make it’s way into our bodies.
It’s just a ton of nuance to put into a single simple phrase. CI/CO is much easier to say then to communicate that label calories =/= calories in the food =/= calories that make it in your body, etc etc.