True, noone can store more energy than you ingest.
But - as the article says - it's very difficult to know exactly how much you're ingesting. The calorimeter is a very blunt way of determining how much energy is "in" food - not only do food labels probably routinely understate how much energy something contains, it has no way of explaining how that energy is actually digested or metabolized by the human body.
Many people calculate their diet based on very slim (~500 kcal) margins. It's conceivable that these are obliterated by these small fluctuations in actual vs labelled calorific content.
That's without getting into issues like insulin sensitivity and so on.
My go-to recommendation for people trying to lose weight is eliminate all sugar and simple/starchy carbohydrates and start a fairly light exercise program. This will have a marked impact on appetite, and most people will naturally start losing weight. If weight loss stalls, start playing around with meal portions and feeding windows.
So far, I haven't heard of anyone who hasn't lose weight with this routine.