In current versions of Drupal, you can configure a multisite install to arbitrarily specify what configuration is shared through table prefixing. For instance, you can have the roles table shared but nothing else, and all your sites will share the same roles but each will be unique for everything else.
This is not currently possible with CMI. Tables can still be shared, but we do not have this concept in CMI. This is (probably) a critical regression right now. Some options
1) Won't fix. We decide that you just can't do that with CMI and punt the problem to Domain or other contrib solutions.
2) If we keep the context system, we can either build context plugins to manage this. This would probably be the sanest approach, however there is currently an issue to remove the context system () which seems reasonbly likely to land and I don't think this is a compelling reason to block it.
3) Implement something new. beejeebus and I discussed an idea that there would be a hierarchy of overrides, and default config gets merged into the levels above until you end up with a full set of overridden config. For instance
There may be more levels. We discussed having an event which could inject overrides as well, but I feel icky about this. Regardless, this is one idea of what we could do. There are probably others.