With the release of v1.2.0, Indigo now supports custom CSS!
To do so, add a file called
custom.css in your site's
/static/css folder (you'll have to create that folder if it doesn't already exist). In that file, you can add whatever custom styles you'd like, and they'll override any built-in styles.
You can see an example of this here, which uses a custom palette as well as additional styling on the updates page; Angelo has written about the motivation for custom CSS in this blog post and shares his own custom.css file.