At the root of this lies the problem that content, configuration and code is stored in one blurp (a single db). Never clearly bounded nor contained. Config is spread over tables. Usergenerated content (from comments to orders) mixed up with redactional content: often even in tables, sometimes even in the same column. Drupal suffers the same.

What is needed, is a clear line between configuration (and logic), redactional content, and user generated content. Those three have very distinct lifecycles. As long as they are treated as one, the distinct lifecycles will conflict. No matter how good your database merging is: the root is a missing piece of architecture.