I can confirm this problem but coming at it from another direction.
I'm using API-Platform and have different DB config values for Dev and Test environments.

Regardless of the environment I specify, only the main .env file is loaded.

actor: ApiTester
modules:
    enabled:
    - Symfony:
          app_path: 'src'
          environment: 'FOOBAR'

So to make things work, I have .env pointed to my test database and rely on .env.test and .env.dev to work correctly in the regular symfony app.

I've tracked the code to my-app/src/Kernel.php where the correct env value is passed in, but .env files are read in the wrong order.

In the course of further research, I discovered that the .env files seem to have the desired affect over the environment value specified in the symfony configuration above. So I'm not setting environment in the Codeception > Symfony module. In its place, using .env files seems to work well enough for both the main symfony stack AND codeception

#codeception.yml
params:
    - .env.FOOBAR


# .env.test
###> symfony/framework-bundle ###
APP_ENV=FOOBAR
...

# tests/api.suite.yml
# no environment specified since it doesn't appear to have any affect
actor: ApiTester
modules:
    enabled:
    - Symfony:
          app_path: 'src'

@ThomasLandauer Can you reproduce this problem in the test project?

I need to know if this is still a problem with the supported versions of Symfony, at least Codeception 4 and version 1.6 of this module.

I am not able to reproduce or fix the problem with the versions described in this issue, so please update it.

Yes, the issue is still there. I created https://github.com/ThomasLandauer/symfony-module-tests/tree/issue_88
Run vendor/bin/codecept run Functional EnvironmentCest:try -vvv, and you'll see "foo" in the output, which is the string I put in Functional.suite.yml.
However, when you open /public/index.php/environment in a browser, you'll see "prod".

This issue will be fixed with version 3.4.0 of the module.
A new config parameter will be added:

# tests/Functional.suite.yml
modules:
    enabled:
        - Symfony:
              bootstrap: true

Then you have to make sure that your codeception.yml file is not loading .env files.

You will have to have an .env.prod file and enable it in the Functional.suite.yml file as well.
You will have to enable the services that are not public for the prod environment in config/services_prod.php, you will also have to enable the necessary bundles for the symfony module to run the tests well (WebProfiler for example) in your config/bundles.php file.

After doing all this you will have to move the necessary settings in your config/packages/prod/ and config/routes/prod/ configuration files.

I'm still not quite clear on the use case where you would want to run tests in this environment, but at least it's already possible to do so.