Your question asks about designing a "server" but it sounds like you are asking whether you need a separate Moodle for each scenario.
Why not install Moodle on an Amazon EC2 instance and try some test configurations? You can easily kill a bad one and then try again.
My experience is that you learn more about how Moodle works by setting up even a simple installation and configuring it, rather than contemplating it in the abstract.
Moodle is very powerful, but some of the concepts (users, courses, contexts) are not completely intuitive at first. Some of your questions make me think that it would be of benefit for you to see concretely how your scenarios might be operationalized in Moodle. It may require some "reimagining" to see how you could do things in Moodle rather than in the hierarchical structures you are accustomed to.
