Depends on the soup. Some soups (including butternut squash imho) aren't that pleasing to eat when chunky. Some ingredients don't hold up to being boiled like that, but are lovely when blended. In cases like potato soup a combined method makes a soup that's both creamy and chunky which is miles better than the chowder you'd have otherwise (same goes for broccoli and cauliflower, you can get a lot of veg into a soup that way).