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.
"Industrially manufactured food products made up of several ingredients (formulations) including sugar, oils, fats and salt (generally in combination and in higher amounts than in processed foods) and food substances of no or rare culinary use (such as high-fructose corn syrup, hydrogenated oils, modified starches and protein isolates)..." [1]
[1] https://en.wikipedia.org/wiki/Nova_classification
I highly recommend Chris van Tulleken's Ultra-processed people for a more indepth read on this fat correlation (excuse the pun :))