Best Workflow for Maintaining Themes?

You can essentially do the same thing: build your own theme component and add that as a child to your base theme (sourced from git). Then you can update the git theme as needed without impacting your custom work in the component.

That’s the simplest way, you might be duplicating some CSS but probably not an unmanageable amount.

More on themes and components: Beginner's guide to using Discourse Themes