The end of the article gets the point. The problem isn't that food is processed; the problem is that extremely processed foods are much harder to moderate yourself on and present a much, much more appealing food to overeat on, which in turn causes health problems and is why so many people are so fat, along with other factors like people being lonely and depressed, and food being a quick and cheap way to make yourself happy, the broad availability of unhealthy food and the sometimes restricted availability of healthy food, the fact that people are too damn busy to find time in their schedules to prepare their own food, etc. etc.
Which itself ties into other systemic incentives. Processed food is shelf stable, fresh often is not, so it's friendlier to logistical systems that deliver everything we eat, which means less of it gets wasted, which means the prices are lower and availability is virtually guaranteed. Put simply: it is far easier and more profitable to ship, stock, and sell potato chips than it is to sell potatoes, and because everything in our system is profit driven, the better things map onto that, the more they occur. Ergo we're drowning in potato chips and still starving.
In that case we can just take Ozempic or whatever guys!
Just kidding, no that's not the problem. The problem is processing destroys/alter many molecules we do not even know about or know it's full "purpose"/role in nutrition and digestion. The commonly talked about vitamins and RDA and such are just the bare minimum so a broad population does not get sick, but does not mean optimum health for a given individual.
Cf. eating 10mg of iron in a steak, readily bioavailable vs eating 10mg of iron from cereal. One is bound in easily digestible compounds, the other is iron shavings or rust.
e.g The British Navy discovering that scurvy is fixed by eating fresh food; ensuring to add citrus to sailors diets, then forgetting about how it worked. Then retrying citrus, but cooking it one using copper vessels, which destroy much of the vitamin C content.