If a MC bean is defined in some component and doesn't need any configuration, the component should provide a sensible beans.xml.
Now if we need a definition which spans multiple components it can go into ejb3_1, but it also means that ejb3_1 should have some tests that verify the integration. What you define, you must test.
For example this one http://anonsvn.jboss.org/repos/jbossas/projects/ejb3/trunk/deployers/src/main/java/org/jboss/ejb3/deployers/metadata/processor/SetDefaultLocalBusinessInterfaceProcessorFactory.java and similar ones really don't belong to the "deployers" nor do i see it being specific to any component expect for a runtime component.
The other one which i guess should belong to the runtime component is the
<bean name="org.jboss.ejb3.EjbReferenceResolver" class="org.jboss.ejb3.core.resolvers.ScopedEJBReferenceResolver"/>
Right now, it's in core.