I noticed that while we do explain that outbound hyperlinks are not publication resources in the term's definition, we don't say that the manifest is only for listing publication resources. Currently, we only say:

EPUB creators MUST list all publication resources in the manifest, regardless of whether they are container resources or remote resources, using item elements.

But this doesn't make it invalid to list non-publication resources. It might be better to make the restriction explicit:

EPUB creators MUST list all publication resources in the manifest regardless of whether they are container resources or remote resources. Moreover, the manifest MUST only list publication resources.

(I ran into this trying to place an epubcheck restriction on listing hyperlinked resources on the web.)