Because then if they need to to any kind of emergency replacement, or just replacement in general, they can hopefully only tear up one side of the road. And there's more under the street than just storm sewer. Not infinite space down there.
Also, manholes sit lower because as they add asphalt lifts they don't always expose the entire ring and add more to lift it up. Or the contractor didn't get the correct elevation during construction, causing it to sit lower.
