It is not that easy. Depending on how and where you read them they might also affect the build.

config/runtime.exs is only evaluated during application boot, therefore its solely runtime config.

What is DB_URL in the system environment?

Do you perhaps have no dockerignore file which contains _build and deps and therefore partial builds slip into your container, which again might cause config values to exist that you do not want to exist?

As far as I know, config/test.exs does not set or overwrite the secret_key_base in a default generated application.

So you might have changed some things for a reason or by accident. It does not make (much) sense to read the env during test. If you do not want to hardcode a secret_key_base in config/config.exs (which is still there) you can remove it there and use config/runtime.exs instead to read it from the env, while hardcoding some “well known secret” in config/test.exs.

Or you just don’t touch the value in the test config and use the one from the “main” config as a well known default, that you shouldn’t use in production then though.