Envision french onion soup: broth and all those slips of onion which are well cooked but have substance.

The onions do not cook down and dissolve/disappear. But if you don't include them there is nothing but watered sauce with little bits of mushroom next to the pepperoni slices. We like our soup to have some body.

Having said that, you can eventually cook onions to the point they disintegrate but that takes longer than you're cooking this soup.