My understanding is that context_id was originally meant to be a security (permissions) context only, but that various package implementors within aD found it convenient to use context_id as a parent link used to model the site hierarchy.
The thread Roger points to would indicate there was never any consensus over the issue. My guess is that you'll find inconsistency from package to package.
This looks like a research item, a good solution should be found but I don't think it will happen by the time the port's finished.
