airflow.cfg can't pull secrets from LocalFilesystemBackend

### Apache Airflow version 2.9.3 ### If "Other Airflow 2 version" selected, which one? _No response_ ### What happened? When starting an Airflow instance or checking a property via `airflow config list/get-value` properties that have the `_secret` suffix return their literal value and the main property isn't set at all. The default values instead are applied. ### What you think should happen instead? According to the docs, the following snippet should retrieve the key `sql_alchemy_conn` from the secret backend (the local filesystem one, in my case) and assign it to the `sql_alchemy_conn` under the `[database]` section. ``` [database] sql_alchemy_conn_secret = sql_alchemy_conn ``` https://airflow.apache.org/docs/apache-airflow/stable/howto/set-config.html ### How to reproduce Reproducing requires only configuring the following properties in airflow.cfg and the .env file in the same directory. The secret backend still works from within a DAG, however, it just seems to not be invoked while parsing the airflow.cfg. I tried bringing the [secrets] section to the top of the airflow.cfg, since by default it comes after [database], but that had no effect. ``` [secrets] backend = airflow.secrets.local_filesystem.LocalFilesystemBackend backend_kwargs = {"variables_file_path": "./.env"} [database] sql_alchemy_conn_secret = sql_alchemy_conn ``` and an .env file (or yaml or json) like this ``` sql_alchemy_conn=postgresql://airflow_user@localhost/airflow_db ``` ### Operating System Arch linux 6.10.4-arch2-1 ### Versions of Apache Airflow Providers apache-airflow-providers-celery==3.7.2 apache-airflow-providers-common-io==1.3.2 apache-airflow-providers-common-sql==1.14.2 apache-airflow-providers-fab==1.2.2 apache-airflow-providers-ftp==3.10.0 apache-airflow-providers-http==4.12.0 apache-airflow-providers-imap==3.6.1 apache-airflow-providers-smtp==1.7.1 apache-airflow-providers-sqlite==3.8.1 ### Deployment Virtualenv installation ### Deployment details venv setup from python 3.12.…