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It is a little confusing

I wonder if you're overthinking things and/or perhaps mixing up concepts based on your questions.

What they are saying is that diets higher in processed foods, especially when a significant number of calories come from highly / ultra processed foods, tend to translate into people who are less healthy and have higher rates of chronic disease.

This isn't saying that all unprocessed foods are inherently healthier than all processed foods, nor is it an attempt to label every specific food item good or bad. The article even addresses that some of these labels (ex: ultraprocessed) are a bit nebulously defined.

Also, it's important to consider the reasons why certain types of processed foods are problematic, as the reason(s) can be different from product to product or even brand to brand. For instance, processing can destroy, neutralize, or even remove important nutrients (ex: vitamins and minerals). Processing may involve the addition of or concentration of salt, sugar, fats, preservatives, and other chemicals that can all contribute to chronic health issues. Some processed foods avoid or minimize these concerns, others seem to embrace them all like it's a competition.

Pasta is not one monolithic thing where all types and brands are the same. Some will be more or less processed than others. I'm surprised grapes would be confusing, if they're raw grapes they're unprocessed, if they're canned/jarred/preserved, then they're processed. I'm not sure what the tofu question has to do with anything, as this isn't about classifying each and every food item as good or bad. People do eat cooked chicken that doesn't have salt, oil, sugar, preservatives added. But even so, raw chicken is one of the ingredients in a lot of at home recipes. In the context of processing wheat into white flour for pasta, most/much of the vitamins and minerals are removed, and the carbohydrates (starches/sugars) are concentrated. It's not really equivalent to removing an organ from an animal. A closer, but not perfect analogy, would be removing those livers, then extracting only the oils/fats/lipids from them ... and then that liver oil would be more akin to a product like pasta or white flour.