Our biological ancestors evolved over 10s-100s of millions of years to consume raw plant matter and raw meat. Only in the last 100k years or so did we start consuming cooked food, which gives some time for evolution to adjust our genes. Our bodies are wet chemical machines that we are confident can consume such food.
These are the unprocessed and moderately unprocessed foods in the NOVA categorization. Processed foods is something that began to be consumed a few thousand years ago (eg. Tofu is 2k+ years old in China), and ultra-processed foods, as defined above, became largely consumed a few decades ago. So there are very good reasons to define these categories as they are. The lines dividing them are fuzzy but that is how all non-physics sciences work.
> ultra-processed as a food category is that it has very little to do with the nutritional value.
Now, if you have a complex system like the human body, it's reasonable to say that the more you drive it outside the domain that it was designed and tested in, the more risk you are taking on the something bad will happen. So a priori you would be mindful of consuming ultra-processed foods. It is a testament to biological evolution that nothing radically bad happens when we consume ultra-processed foods. But it seems very reasonable to investigate such foods more carefully for smaller but long term impacts on health.
> little to do with the nutritional value.
The digestive system doesn't just care about raw nutrition - the number of proteins/fats/carbs - of the incoming food. There are a number of physical and chemical processes occur during digestion, and these processes can be sensitive to what combination of things go in and in what physical form, etc.