Sure but then what is your alternative for easily assessing in a reportable way what the energy density of a food is? Bomb calorimetry doesn’t say “you will get this amount of energy from a food”, it simply says “a gram of this material has about this much energy density.” Evolution has done a remarkable job of maximizing energetic recovery from compounds, and it’s simply true that eating more energy in the form of food than is used by the body will result in the body storing said excess energy. Kcal is a convenient relative metric that does correspond to this phenomena. That is objectively true. Is it exact? No. Does it claim to be exact? Again no, but you can calculate the yield by looking at digestive and metabolic processes within constraints and the relative amount is still useful as a gross measure.
It’s fine to say that kcal aren’t what we eat. But then food isn’t really what we eat either. Food is simply compounds that our body can use to perform chemical work. You can quantify this work. And you can use a word other than work to describe chemical reactions, but the semantic point is conserved regardless.
A good proxy for this general capacity in a human body from organic digestible material is kcal. If you have an alternative to this that is easily calculated and also easily understood, I’d recommend writing it up and submitting it to a nutrition or medical journal, where it can be peer reviewed, and if it holds merit, published, to be more broadly examined, and perhaps adopted.