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 3.12.4
`pip install "apache-airflow[celery]==2.9.3" --constraint "./constraints-3.8.txt"`

### Anything else?

This is from a completely fresh installation. The issue also appears on an ARM Mac. I don't have the other possible secret backends set up, so I don't know how those behave. I can also understand that this might be a documentation issue and this isn't supported anymore, since the secrets backend would be retrieving secrets for the same file it is configured in itself.

### Are you willing to submit PR?

- [ ] Yes I am willing to submit a PR!

### Code of Conduct

- [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md)

Start by reproducing the behavior with the shown airflow.cfg and .env, then inspect the airflow config list/get-value entry points and LocalFilesystemBackend handling. Done means the [database] sql_alchemy_conn_secret setting resolves sql_alchemy_conn instead of returning the literal suffix value and applying the default.

Written by the indexing model from the issue text.