This is a good observation. Yogurt for example is now something one buys packaged from a grocery store, after milk was pasteurized and deliberately (re)inoculated with the right mix of bacteria to induce lactic fermentation. This of course can occur naturally, but now we do it in a controlled and safe manner and thus is now a "processed food". Well, of course there are those that come with added "fruit" (not really). Same with Sauerkraut and even originally the curing of meats (Salami, Chorizo, de-hydrated meats, etc).
And that is different from most packaged, canned, boxed, foods which are clearly manufactured as they just wouldn't happen otherwise, in the way that ingredients are mixed and put together with the primary goals of making a product hyper-palatable (it sells), at lower cost and with a long shelf-life (minimizes risks), and only incidentally if at all, with any care for its nutritional value, in which case they throw in whatever fortifications will allow the vendor to claim certain nutritional benefit while not affecting negatively their ability to sell. These tend, as you mention, to just add sugar, fats and salt, in a way that one simply does not find in non-manufactured foods.
As they say, context matters. For example there are many who believe that salt intake by itself is not the problem, instead the optimal ratio of Sodium to Potassium is what becomes problematic. In latter years with all those added salts, Sodium intake has increased, while the lower share of natural foods has also meant a reduced intake of Potassium, throwing us off-balance from what a "normal" body needs.