Can I create a completely customized theme template in the authoring tool?

Yes, you would do that by using the theme builder. It allows you to easily apply a universal style sheet to every screen in your course. You can find the theme builder in Course Settings in your course workspace or the sub-tab in the orange Administration tab in the tool. Once you are in the theme builder you need to select a theme to activate and then you can upload your logo, customize the fonts, colors and even customize the navigation buttons.

You can find a short tutorial on how to customize your theme here.