I think that is happening. A co-worker had a course that she never visited and it appeared first in the my courses list. It wasn't until she visited the site that it moved from the first spot in my courses. Maybe I need to figure out how to identify those courses with a special color like your image.
Either way, this small change made life a bunch easier for our teachers so that the courses they use the most are automatically sorted for them! It's also nice that it's right on the homepage and the courses are big tiles and easy to see.
We keep a clutter-free homepage.