Hi,
I understand it's a matter of principles, so this is only my two pence. I prefer the docker-compose file because I have a single configuration file to maintain and backup. Since I have to modify the docker-compose YAML file for username, password and volume name, it's more convenient to also add the local path of my shared folder, instead of having two places where to set configurations
About the webmin, since, as I understand, it "just" parses and updates the apf.conf file, it could stay in a container by itself, as an additional service in docker-compose accessing the netatalk apf.conf via a shared folder, this is what docker-compose is for. No need to put it in the same Netatalk container.
I hope this helps