Yes, by default, configuration options with an existing environment variable must be changed via environment variables. During container startup, all supported environment variables are used to create a config/overwrite.config.php inside the container, which is always used instead of the default config/config.php. Therefore, changing config/config.php will never work, same applies to config/overwrite.config.php.
If you really want to include a custom configuration file and not use the environment variables, you must ensure that this file is loaded last (configuration files are loaded in alphabetical order, last option wins), e.g. by mounting your custom configuration file to config/zz-user.config.php.