If there is a lot of difficulty in creating different access systems for different boards on the Zone, a brute force way to accomplish this might be to simply have two completely separate Zones, a public one with public subjects, and a private one containing only boards like Community, SF, etc.
It would mean moving from one to the other if you were changing boards a lot, but with the ability to “remember” a login, it shouldn’t be too hard.
Then each board could have completely separate security protocols, and membership restricted or not restricted. Software changes on one should be easily transportable to the other, and except for the basic access differences, the code should be no different.
Just an idea.