Putting aside the vague hand wavy definition of what "highly processed foods" literally means, my suspicion is that there are two things making processed food worse for you.

I've heard drinking juiced fruits is worse for you than eating the equivalent fruits, as the sugars in the fruit are wrapped in fiber that make the sugars "slow release" into your body, and those are broken down when juiced so the sugars hit you at once. I suspect processed foods "mainline" nutrients in ways that unprocessed foods don't.

Secondly, I think a lot micro-nutrition is ignored when comparing processed food, like the fat, carb, salt, etc is equivalent between potato chips and, say, a baked potato with butter, but there are a lot of small things that our body needs that are not part of that equivalence. At least for me, when I eat potato chips I eat more because they never quite satisfy me. I suspect this is because the micro nutrition is cooked or processed away, so I end up eating more carbs because it's not quite giving me all what I need, just the big macro needs.