There is currently limited support for keeping a subset of data synchronized (we have plans to improve this) - if you're using the client libraries in an app, we've focused on supporting the common case of keeping all the data per bucket for a user synced. In the case of keeping all data mirrored to a backend, we provide an endpoint per bucket that you can listen to all changes for all users so you can keep the entire data store synchronized.
With keeping the objects on separate timelines, do you or can you run into any problems with CoreData inverse relationships? I'd be concerned that my objects would have issues where a change got synced for object A that had it linking to object B, but somehow my application crashed before it got the synchronization for object B sent. I can imagine various reasons why this concern is stupid, including "saurik doesn't understand how CoreData works" (as I only even learned of its existence a couple days ago).
Core Data relationships (including their inverses) that come over the wire can be lazily resolved by Simperium if necessary.