It depends on the article - as we've come to know it depends on the article contents and is usually the result of broken WYSIWYG tags. But as you've noted, and is one of the strong reasons for such a feature, this problem would not exist if sections were actually stored separately rather than implied by the editor contents. However, it would be a significant change, so we will not see it until 4.1.
If you can provide more information about the problematic article, I can see if additional workarounds need to be implemented to prevent broken tags from interfering with detection.