Airflow 3.0.6 ignores logging settings, only outputs to STDOUT

### Apache Airflow version

3.0.6

### If "Other Airflow 2 version" selected, which one?

_No response_

### What happened?

This is a new install. Despite any settings in the config OR the command-line, I can't get it to log anywhere but stdout.

In the config:
logging_level = WARN
fab_logging_level = WARN
base_log_folder = /airflow/logs/
[logging]
base_log_folder = /airflow/logs
logging_level = DEBUG
logging_level = WARN

Tried: ExecStart=/bin/bash -c 'export AIRFLOW_HOME=/airflow ; source /airflow/airflow_env/bin/activate && /airflow/airflow_env/bin/airflow api-server -l /airflow/logs/api-server.log'

Also tried:
ExecStart=/airflow/airflow_env/bin/airflow api-server -D --access-logfile /airflow/logs/webserver_access.log --stderr /airflow/logs/webserver_error.log

Also tried:
ExecStart=/airflow/airflow_env/bin/airflow api-server -A /airflow/logs/api-server.log --access-logfile /airflow/logs/webserver_access.log --stderr /airflow/logs/webserver_error.log

The only output is stdout. Running it from systemd dumps this in /var/log/messages and it's very difficult to parse and read

### What you think should happen instead?

Doesn't comply with documentation.

### How to reproduce

In the config:
logging_level = WARN
fab_logging_level = WARN
base_log_folder = /airflow/logs/
[logging]
base_log_folder = /airflow/logs
logging_level = DEBUGlogging_level = WARN

Tried: ExecStart=/bin/bash -c 'export AIRFLOW_HOME=/airflow ; source /airflow/airflow_env/bin/activate && /airflow/airflow_env/bin/airflow api-server -l /airflow/logs/api-server.log'

Also tried:
ExecStart=/airflow/airflow_env/bin/airflow api-server -D --access-logfile /airflow/logs/webserver_access.log --stderr /airflow/logs/webserver_error.log

Also tried:
ExecStart=/airflow/airflow_env/bin/airflow api-server -A /airflow/logs/api-server.log --access-logfile /airflow/logs/webserver_access.log --stderr /airflow/logs/webserver_error.log

The only output is stdout. Running it from systemd dumps this in /var/log/messages and it's very difficult to parse and read

### Operating System

alma Linux 9

### Versions of Apache Airflow Providers

_No response_

### Deployment

Virtualenv installation

### Deployment details

_No response_

### Anything else?

_No response_

### Are you willing to submit PR?

- [x] 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)

No source file or test is named. Start by reproducing the api-server behavior with the shown configuration and command-line options under systemd, then trace the api-server logging entry point and its documented flags. Done means the configured logging level and file destinations are honored instead of all output going to stdout.

Written by the indexing model from the issue text.