I think you are on the right track just some details need to be worked out.
In order to keep grading for each course separate, all graded activities must be in the individual courses not the metacourse. Metacourse should have only the shared materials.
Students will be visiting either their individual course or the shared (meta) course, depending what they want.
You might have thought that materials from metacourse show magically in other courses. That is not the case. However, it is possible to place in the individual courses direct links to the materials in the metacourse to make things a tad simpler for students. I just advise to do that in a separate topic and label clearly that these are links to the shared course, so students don't get a shock that they are suddenly in a different course.