So, from what I understand the best way is to keep everything separately.
Main server for running Discourse. Then a server for PostgreSQL and S3 (or any other object storage service) for uploads.
The app.yml file seems to me that it doesn’t change often, so you only need to save it once. Or at most a few times during the month.
This allows you to make backups of your files, even in a more organized way.
If so, I find that their choice not to implement multiple daily backups in the core makes sense. On the other hand, those who have complex needs will certainly make particular configurations like that. And in the end you just need to redo the installation(with the app.yml saved somewhere) and then reconnect it to the database and to the S3 for the data uploads. The backups are in those 2 servers separately, so it’s easy to manage for me. I find it a very fair solution.
Thanks everyone for the explanation.