Hi Danny,
Sorry for taking so long to reply - busy busy busy.
Perhaps backwards compatibility was the wrong phrase to use. It was more a consideration of consistency to make things easier for people to find what they're looking for. Although we don't need to make user interfaces backwards compatible in the same way we do for APIs, people don't like change - we are creatures of habit.
Remembering that the list of courses is limited to not show all courses, just the top X (IIRC, by default X = 20); if we remove the currently active course from the full list of courses, this will make space for a different course. We're now showing courses 2-21 instead of 1-20. So if you're on the front page, you'll see courses 1-20, but if you're on a course you'll see 1-21 minus the course you're currently in if it's in the last of 20. If you're in a course not in that 20, you'll see 1-20.
I wouldn't say that this is a case of over-engineering, but trying to consider the user needs and pains. As I say, people are creatures of habit and we don't like it when things change. Equally, we don't like it when we sometimes have to look in one place, and sometimes in another for the same content. I disagree that it is more complex in terms of real people. As a developer you see it as superfluous, but as a user you might not. Going by your argument, Microsoft should remove any button from the Menu and context menus of Word, if it appears in the ribbon.
I'm still confused by your issue with this change, but glad you appreciate the work we do.
FYI, this change was made while I worked for Lancaster University after users finding the previous menu unusable if you were enrolled in a significant number of courses (scroll of death related). Some users still preferred the full list of courses - as I recall, it was students in particular who wanted to navigate between several courses and didn't care which course they were currently in. I think they were largely arriving as a result of targeted e-mail (e.g. forum, assignment/grading, etc) and then using that as a launch point to their next task.
Best wishes,
Andrew