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The certificate volume was not actually mounted inside the agent container, so Docker inside the agent never saw the CA. Create the CA certificate directly in the container at /etc/docker/certs.d/[mydomain.com]/ca.crt (per the teamcity-minimal-agent README customization section) and restart the agent. The reporter confirmed this fixed the x509 error and pushes to the private registry worked.
Source: https://github.com/JetBrains/teamcity-docker-samples/issues/9
Source: https://github.com/JetBrains/teamcity-docker-samples/issues/9