You should either use config files ($HOME/.ttn.yaml and $HOME/.ttnctl.yaml), environment variables or command line flags to configure ttn and ttnctl respectively.
For Docker-based deployments it is common to use environment variables passed to the container in docker run or through a docker-compose file.
The trick with Docker containers is that they run completely outside the scope of your host computer, so they will not have access to the yaml files, nor the environment variables. Read the Docker documentation if you haven't done so already.
OTAA devices don't have a DevAddr nor NwkSKey/AppSKey yet, because they're not activated yet. Have a look at the ttnctl join command to simulate a join, or register a personalized device with ttnctl devices register personalized.
For ttnctl I suggest to just follow the quick start guide.
The ttnctl uplink and ttnctl join commands will be removed from the "public" version of ttnctl and will only be available during development. This is also the reason why it's not in the quick start.