I say that up-front because there are a bunch of people out there who think that the basic science of calorie counting is wrong; that there are other hidden factors that keep some people thin and make other people fat.
BUT, what is true--and which this article highlights--is that calorie counting is super hard to do. As a system, it's hard "operate". You can't make mistakes, like forget to enter a meal or a snack, or forget to properly record activity. And it's kind of miserable to live that way. That's probably one reason it's mostly professionals who really do it well.
In software terms, calorie counting has terrible UX. And our food system has bad defaults. The cheapest, most heavily-advertised food is often high in calories per volume.
And of course calorie-counting does nothing for your nutrient intake, which is arguably more important to think about now because foods across the board (i.e. even organic kale) seem to have falling nutrient content.