Isn't your own linked thing contradicting you?
"The Bottom Line
The calculated number of calories in a food or meal assumes you’re able to digest and absorb all of the macronutrients, which is seldom the case. You likely take in fewer calories when you eat whole foods, foods high in fiber and resistant starch, and foods that are uncooked and haven’t been exposed to heat. Now you have another reason to add more whole, unprocessed foods to your diet."