The article seems to contradict that - unprocessed foods are the hardest to estimate. Pounding, grinding, cooking free available calories, bringing them closer to the published number.
I'd say portion control is a bigger problem than any of the things you just listed.
The amount of effort it takes your digestive system to process raw chicken vs. cooked chicken is obviously different, but the fact that they chose to focus on these issues doesn't make them more impactful than portion control.
I was thinking in terms of cooking at home versus going to eat at a restaurant. Restaurants are far more egregious in terms of being calorific as well as highly variable and prepackaged food usually isn't that good for you.
