The directories config and log are create by docker automatically in the same directory, where you executed the docker run command.
But JTS3ServerMod doesn't create config files on the first run. You have to create them on your own. Here is a basic example, what should be inside of your config directory:
https://github.com/phaldan/docker-JTS3ServerMod/tree/master/config
This part is also described on the docker hub page of my docker image:
https://hub.docker.com/r/phaldan/jts3servermod/
But JTS3ServerMod doesn't create config files on the first run. You have to create them on your own. Here is a basic example, what should be inside of your config directory:
https://github.com/phaldan/docker-JTS3ServerMod/tree/master/config
This part is also described on the docker hub page of my docker image:
https://hub.docker.com/r/phaldan/jts3servermod/