Your consequences of processed food does not seem to be actually be anything inherent to processed food. If there is some chemical (likely fiber in your examples?) that is causing one form of food to have a different effect from another, then that can be artificially processed into the food as well.

The real issue with processed foods tends to be that their goal is isolating the tasty by removing the healthy. If you actually set up the correct goals, then there is no particular reason why "natural foods" could not have their effects artificially replicated or improved upon.