How can I set up default settings in Kibana / Docker?

Is there a way to do this? I mean settings as in using the dark theme, index patterns, etc.

You can do so with the kibana.yml file as of 6.5: https://github.com/elastic/kibana/pull/21628.

Your configuration would look something like this:

uiSettings:
  overrides:
    "theme:darkMode": true