Your answer is sufficient. So this course is about using GH through Git not using the GH interface online, right, so it really is NOT about GitHub, eh? Therefore, this course is equally applicable to any other repository site, isn't it? If that is the case, this course should be renamed Git Real 3.
Given this, I would urge Code School to produce another course for GitHub. Why? You can do a lot of stuff directly on GitHub, including editing text files and so on, things that are useful for students to do and understand. It's not all easy to understand on GH (let alone Git).
You could, as part of the course or separately, introduce alternatives to Git Bash, introduce GitHub Desktop and alternatives to it (which are listed on git-scm.com), and then delve into how to use GH Desktop, or one that is more user-friendly. I've just heard that GitKraken is pretty easy to use but haven't yet tried it.
Again, the point is that why call it Mastering GitHub if you're just continuing to use Git?
Good! I need that!