Firstly, it assumes that we haven't evolved since modern agriculture, which of course we have; people with ancestors from areas with grain harvesting have more copies of the amylase gene, which produce enzymes that help us to better digest calories.
Secondly, it assumes that the "priority" of evolution in paleo times was to optimize our health in our current environment. It wasn't. Our hunter and gatherer ancestors were starving; we were optimized to extract every last calorie from our food. So when simple starches like wheat came around, we evolved to have more copies of the amylase gene - something that does not help us today.
The paleo diet works precisely for the opposite of the stated reason. These are foods that our bodies are not evolved to perfectly digest. Uncooked foods are far enough in our evolutionary past that people on raw-only diets consistently lose weight, even if they eat a lot. If they were on the savannah they would die.
I'm not saying the diet itself can't be great, just that the entire article could be fodder for Penn & Teller.