For a large part this is an architectural issue.
It would extremely useful if it were possible to test a plugin on the production database in a development or staging environment.
That's not possible when NodeBB gets the list of activated modules from the database.
We have a similar problem like this with Drupal7. It's close to impossible to test something on the production data without making a copy (which is extremely unpractical with a large DB) because of the tight coupling between configuration and content.
Haven't used it yet but Drupal 8 has improved on that issue quite a bit:
https://www.drupal.org/docs/8/configuration-management/managing-your-sites-configuration
