The Harvard blog simply makes a statement without actually providing the proof.
And there's also the point that calories that "leave the body" aren't really calories consumed.
So if a portion of the raw caloric value of something gets expelled through waste because we aren't really able to process it in time, then it's not really a consumed calorie.
A large portion of the rage against Calorie In Calorie Out is really about our ability to accurately measure calories in any fashion.
We make estimates about the caloric value of a food because the means by which we can measure it is destructive. And we assume that every calorie that enters our body stays there until used as energy. Which may not be true either.
And the WebMD article specifically mentions that the low carb group was essentially stressed the whole time. And it's a study of 21 young people who lost 10% to 15% of their body weight. That's 10 - 20 pounds of an average person.
This guy lost weight eating 1800 calories of twinkies a day. https://www.huffingtonpost.com/david-katz-md/chewing-on-the-...
I think this is a much more interesting experiment as twinkies are roughly uniform. There may be some caloric variation, but none so great as to be relevant. Plus, the overs and unders should average out.
So watching the caloric content of your food is always a good idea if you're looking solely to lose weight. But instead of trying to figure out how many twinkies you can eat in a day, we should be trying to find out which foods we can eat a lot of and still maintain a caloric deficit.