You can engineer healthy food. The problems isn't the processing. Its that most people who are engineering food do not have "healthy" among the goals.
We're conflating "designed" with "designed recklessly".
It matters because a lot of people can't afford the diet suggested here. The messaging needs to distinguish between adding protein powder because there's no meat available, and living on Cheetos because there's no meat available, and "highly processed" fails to do that.
The latest conclusion seems to be that the deadly combo is ultra processed foods with high calorie density. That’s what causes us to overeat garbage. Ultra processed low calorie foods are often still junk, but not what is killing us.