But still, I think it does not fully solve the architectural issue or encourage good architecture (though it can certainly help reduce bugs)... In this case you may end up with lots of duplicate instances in different blackboxes which may not be a good thing either.

The point of good state management is to ensure that each instance has a single home. As soon as you start passing instances between functions/modules/components, you're leaking abstractions between different components. Sometimes it is appropriate to do this, but most of the time it's dangerous. Components should aim to communicate as little information about their internal state to other components as possible.