The article name is "Scientists are learning why ultra-processed foods are bad for you", the opposite of this thread's title. Everyone's ignoring the elephant in the room: fiber. Fiber locks up calories and makes the body miss a lot of them, or absorb them later in the digestion process. If we reduce the word "processed" to a single action, it's removing fiber. It's turning wheat berries into flour. It's ripping off…
Humans are extremely efficient at extracting energy from food, regardless of the fiber content. We owe our survival as a species to it, as food was much less plentiful in the ancestral environment.
I've heard of fiber meaningfully affecting insulin response to food, satiety, and some other things - perhaps even gut microbiomes - but not metabolic efficiency.