In the section "Contained Resources" on the page for the Reference datatype, we see that contained resources can reference their containers using the special "#" syntax:

(begin quote)
For a resource that references the container, the reference is "#", like this:

<Patient xmlns="http://hl7.org/fhir">
  <id value="something"/>
  <contained>
    <Provenance>
      <!-- no id necessary (though still allowed) -->
      <target>
        <reference value="#"/>
      </target>
    </Provenance>
  </contained>
  <!-- other attributes -->
</Patient>

(end quote)

However, the invariant ref-1 states:

reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))`

The part reference.substring(1) will in this case result in the empty string, which will not be found in the %rootResource.contained.id collection.

So, I think the business rule will trigger for this kind of reference, and we should adapt ref-1 to make this possible.