Drupal Distribution best practices
Once your features are overridden, then the configuration is moved from the files to the database (i.e. Drupal no longer looks for the configuration supplied by the feature module and uses your configuration in the DB). This means you can update the files without overriding your changes/additions (Just don't hit the revert button in the Features admin UI). That being said, if you changed/updated a content type, you will no longer be able to take advantage of any changes/updates that were made to the commons distro supplied content type. This is the same for views, contexts, rules, etc.  Some devs will use the Features Override module to allow them to store their site specific overrides in a feature.  This allows you to store your overrides in files and still leverage any changes/additions from the distro.