I actually think Dan did a good job with '/course/format/renderer.php' despite my initial 'panic mode on, need to support this and users are protesting' issue. It makes it a easier for me to support core changes automatically as I only over ride what I need to in the course format.
I think that the confusion comes from the fact that '/course/renderer.php' renders the components of the course which are overrideable by the theme, but it is the course format that defines the layout and as little styling as possible by overriding '/course/format/renderer.php'. Themes and course format's share a common goal but do need to be separate because theme's style and perform overall layout, course format's just layout courses because you always want a 'corporate image' and way of doing things across all courses but want at the same time to have separate layout templates for the individual courses.
I hope this makes sence!