The rule for references is that "old points to new, many points to one".  MessageDefinition would need to exist before an activity or plan definition could reference it, and the same message definition could be used by many activities or plans (and in general, a single ActivityDefinition or PlanDefinition.activity would only be associated with one MessageDefinition).  On this basis, the PlanDefinition and ActivityDefinition should point to the MessageDefinition, not the other way around