Configuration via ./discourse-setup is a way to support novices to get discourse up and running easily.
For any advanced usage, you will configure a container editing yml config files in the containers directory.
./discourse-setup creates containers/app.yml for you, which you can use as a base config for other customizations.
If you are asking to automate further customizations, this thread might be helpful: Initial configuration directly from `app.yml` (discourse-docker / INSTALL-cloud.md)