This is a result of how Docker handles bind mounts for volumes (with ‘normal’ volumes, the volume is auto-populated with the contents of the directory in the container image on volume creation, but for bind mounts, it does not do this).
There’s a PR open at Provide better handling of config files in Docker containers. by Ferroin · Pull Request #12310 · netdata/netdata · GitHub that will fix this for newly created containers using bind mounts. It hopefully should be merged in the next few days tops (and definitely before the next stable release in two weeks or so).