"Twenty calories, after all, is a bite or two of food, ... an absolutely trivial amount of overeating that the body then chooses, for reasons we’ll have to discuss at some point, not to expend, ... , so that we don’t overshoot by 20 calories a day. ... That’s matching intake to expenditure with an accuracy of better than 1 percent."
The author, despite his qualifications, is numerically illiterate. Anyone who has seriously worked with numerical data understands the law of large numbers. If my body works to maintain some caloric level e, then over time the full meals I skip for seemingly no reason, or the second helpings I mysteriously decline, amortized over a scale of months, will balance out my caloric intake with severe accuracy. (Assuming I am predisposed to maintain a specific weight.)
Secondly, stating that weight gain is due to eating more calories than you burn is neither tautological, vacuous, nor inane. It might not be satisfying to the author, but it is a cogent and useful explanation of why people gain weight. Other, worse examples that institutions might give that would give people fewer clues about how to combat weight gain: "you've angered some god," "you're predisposed to be fat," "you're eating the wrong kind of food." The link expressed between consumed calories and stored mass is not logically trivial. Stating that I should eat fewer calories clues me in to track and reduce the calories listed on the side of foods I buy. If you want to get pedantic, a tautological explanation would be you're getting heavier because you're gaining weight.
It isn't worth dissecting the rest of the article. This guy doesn't know what he's talking about. He wraps up a lot of obvious points in a lot of science that he doesn't understand.
P.S. - it isn't a mystery to anybody why people get fat