It uses spoor extension to communicate completion to LMS one of two ways - by course completion (usually navigating through to the end) or by assessment pass. In your case, ensure your tracking in spoor is set to course completion.

If you've structured the course into pages, I'd imagine it should mark course complete if you make all pages optional but set up a required page at the end (so that all users end up at the same finishing page after the 3 pathways). If you have a menu, you may need to use some css to hide this last page.