The spec says:

Resources referenced from the link element are publication resources only when they are:

• referenced from the spine; or
• included or embedded in an EPUB content document (e.g., a metadata record serialized as RDFa [rdfa-core] or as JSON-LD [json-ld11] embedded in an [html] script element).

In all other cases (e.g., when linking to standalone [onix] or [xmp] records), the resources referenced are not publication resources (i.e., are not subject to core media type requirements) and EPUB creators MUST NOT list them in the manifest.

Currently, EPUBCheck reports OPF-067 ("The resource "…" must not be listed both as a "link" element in the package metadata and as a manifest item.") even for the two exceptions listed in the spec. For instance, spec example 33 (reference to a record embedded in an XHTML content document) is rejected by EPUBCheck.