@mladen Yes the template and the dashboard still requires you to run the setup command to make them available. Its a known issue and we are working on it.
Just one more question, is it possible to use metricbeat key-store and put variable in management.yml file instead of plain text?
Yes you can do that, you can add secret to the local keystore and reference them in the config management. We are considering allowing config management to send a keystore to the running instances.
FYI: The token that config management is using on the beats to connect to the API is already stored in the keystore.