The sections in the non-canonical HTML document need to be able to be addressed by a fragment identifier. The same identifiers need to appear in the same places in the XML. These fragment identifiers should follow a predictable format so that someone referencing a section in an RFC can create the fragment without needing to read the XML or HTML if they know the identifier format chosen.
If an author has supplied XML with links to anchors, those anchors should also appear in the non-canonical HTML document.
These anchors will be reflected in the final XML, HTML, and possibly PDF versions of the RFC when it is published.