Teaching with Moodle
Is metacourse an answer?
I would think so, but there is an issue if you are allowing students to select parts of their course of study. For example, if everyone in metacourse A is enrolled in 6 compulsory subjects and only three are enrolled in one group of 6 electives while another three are enrolled in another group of 6 electives, that is going to make it difficult.
Another element is if a person enrolls to take 1 course, they can only be enrolled to take that one course, and must not be allowed, even mistakenly, to be enrolled in a certification grouping of courses. Looking at how this could be done may be simple.
Single course enrollments are automated already you say, they can be enrolled into metacourse 1. This allows a student to take Underwater Basket Weaving as metacourse 1 points only to that one course. Certification enrollments can become simplified as a student is enrolled in metacourse 2. This enrolls the student into Underwater Basket Weaving as well as Training Racing Sea Horses, Squid wrestling and so on as that is where metacourse 2 is pointed.
Enrollments go where the metacourse points them, so all you need do is make sure the metacourses are aimed correctly and students can't get mixed up.