Personally, separate courses for me. My logic is that if you ensure that all the mandatory parts are in one course, people can work their way through them without making any decisions about what they can choose or not. It's clear that this whole course must be completed. For the second course, it also becomes clear that they need only complete 1 to 4 topics. I would suggest that even with that clear instruction, users will do all four or just one. Those who can't read will do all four, those who can will just do one. I would word it like Select ANY TWO modules from this course. For EXTRA CREDIT, select a third, something along those lines, depending on the wriggle room I had. This actually reduces their choices, which is what you want, really. Give people too much choice and they will either do the minimum necessary, or do it all, uncertain they have read the instructions right. In either case, they are not really making a decision at all, they are just doing what they would normally do, what their character tells them to do. Create a clear expectation of what their real choices have to be, they will comply.
By giving them the opportunity to voluntarily take on another unit, you create the opportunity to reward effort, and that has to be a good thing.