I'm not saying they're healthier simply because we've historically eaten them.

But there are many reasons to believe natural/traditional foods may be safer and healthier than new industrial foods. To name a few:

1) There's reason to believe our bodies may be more adapted to eating natural or traditional foods, having eaten them for hundreds of thousands of years rather than one or two generations.

2) Many highly processed foods have within decades of their introduction to our diet been found to be really bad for us. Refined sugars, refined oils, refined flours, artificial sweeteners, many of the weird additives, many synthetic compounds like methylcellulose (someone close to me is extremely sensitive to this one), on and on.

3) These new ingredients, new kinds of refining and processing, and even synthetic food compounds, do not have to undergo any rigorous testing to be shown to be safe before being added to food. Even if they do some studies for some of them, how would you really know it's not causing serious long term problems for say 1% of people? Or even 10%? The size and duration of a study you'd need to find them to be safe would be expensive and they generally don't do it, since they're not required to.

4) These new ingredients often introduce novel molecules to the body that the body may not be adapted to. I hope I don't need to explain how many novel molecules that were invented and widely used in recent decades have proved to be highly toxic.

5) We have a huge increase in severe chronic disease in recent decades. I won't claim here that this is primarily because of the changes to our diet from industrially processed foods, but diet is a top contender given that it's one of the biggest things that has changed in the human lifestyle, along with all the other novel substances our bodies come in contact with now.

6) We know of tons of people who were healthy to age 80, 90, 100, eating primarily/entirely natural foods. We don't yet have any examples of this with people eating a large portion of modern industrial foods that didn't exist 80 years ago. This is not proof that they're dangerous, I'm just saying we don't know and have reason to be cautious.