Not at all. "Very warm" is wrongly constructed in English, as it is in fact "hot". You never say "very orange" for red. Hot is how you take the soup (those that are hot). Warm is when it cooled. So if the soup should be taken hot (many are, and many are not), take it warm is unpleasant.
Yes I agree I would never use very warm in a positive way, maybe the soup is gazpacho and it is a complaint. Though even then I would tend to use too warm rather than very warm. Using very with a middling word just seems wrong. I would rather say nice and warm to emphasise somethings warmth.