How Core Data represents sub entities in the SQLite store is an implementation detail that is hidden from you and subject to change. Do not depend on it working one way, because at some point it may work completely differently.
You may be prematurely optimizing. Build it, test it, and if there is a performance issue stemming from how you're using entities address it at that point.
As to your actual broader question wether there should be performance advantages in using multiple configurations for a single store: There shouldn't be. If you have one SQLite store and there is only one configuration, Core Data is not going to be making additional optimizations based on the (single) configuration.
Much of Core Data's performance comes from your data model design and access patterns. An application that is architected to be aware of Core Data faulting behavior that uses a well thought out data model will be quite performant. Even if you have a less than optimal data model Core Data can be very fast if you optimize your round trips to the persistent store (i.e. managing faults, batch faulting when appropriate, implementing a correct find-or-create).
The Incremental Store Programming Guide contains a very good description of how faults are fulfilled. The Core Data Programming Guide has a higher level description of faulting, and discusses batch faulting, prefetching, and the find or create pattern.