There are several ways to manage the drupal site configuration in Drupal 8 either by keeping it in the database or managing it at from the file system or managing with features.
I have launched couple of sites with the combination of the following best practices with managing features and configuration in file system
User Roles and Permissions are being managed by the Configuration Management because features does not export the permissions with the Roles
Using features for managing the other entities and rest of the stuff.
Below the screenshot of attached site structure of one my project