This is a great question. You’re correct in that the credential.helper is stored as an environment variable GIT_CONFIG_PARAMETERS in the job environment. It may be as simple as ensuring that environment variable is properly passed into the container. If you are using the docker-compose plugin, you can set the propagate-environment option on the plugin config to true, and this should propagate the variables set in the job environment into the container.
If that still isn’t working, it may be helpful for us to have a look at some example builds. If you’d like us to take a look at those builds, you can reach out to support@buildkite.com and we’ll be happy to continue troubleshooting there as well!
I’m also curious - why are you needing to perform git operations within the container? Are you not able to perform those operations outside the container in the job environment, and then mount the directories into the container?