Comparisons and advocacy

It's been a while since I looked at this, but from memory,
Step 1. Create a single database. This includes all Users, all Organizations, all Independent Users, and populated by all the courses to satisfy the requirements for each of them.
This is the tricky part.
Step 2. Create a number of different Moodles one for each different Organization and Independent group.

• • Each Moodle can be served from the same server and the database can either be on the same server or a different server, there shouldn't be any difference, but... maybe a separate server would be in the best interests of the clients.
  • Each Moodle is aimed at the database, but as permissions are granted within each Moodle there is no crossover permissions. The only issue that may occur is if a course needs to be edited to meet a common or standard changing requirement. If an Enterprise wants to include something that other Moodles do not need, then a separate course can be made.  
  • Each Moodle requires its own cookie label, eg. ent_001, ind002, ent_003 and so on. This allows any user to be able to access any of the Moodles simultaneously, a handy trait.

This is by no means a complete description, but it is something that has been discussed before and should provide an outline for what you are describing here. Others more familiar with this concept may want to chime in here and discuss this in greater detail. There is an alternative, but it could mean your Moodle becomes overloaded depending on how big your eventual client database is or security permissions are a bit dodgy or some such. 

Good luck.  

Check out IOMAD: "An open-source multi-tenancy solution with Moodle under the hood"