WikibaseServices provides instances of data access services. Those of service for which the "dispatching pattern" applies, should use instances provided by the configured DispatchingServiceFactory instances.
Dispatching pattern here means the pattern when there is an instance of the service that has the knowledge of service instances configured for single repositories. Dispatching service delegates its actions to repository-specific instance based on the input. See DispatchingEntityRevisionLookup or DispatchingTermBuffer for examples of services following this pattern.
The "outer" container will itself provide services to which the dispatching pattern does not apply.
In the long run, use of DispatchingServiceFactory in WikibaseRepo/WikibaseClient should be replaced in favour of the WikibaseServices container.