So that you have access to your backups via a command line restore before you restore your backup. Otherwise, you have to set up an admin account and then configure S3 and then restore. Similarly, whatever settings you put in your database get overwritten when you restore the database.
I think that best practice is to configure S3 only via ENV variables in the app.yml file. It would probably make sense to make them be hidden settings, if not for hundreds of people who would be surprised that they had disappeared.