I agree that it would not be appropriate for an unpack tool to generate new xhtml for the cover and handling it via metadata is the most sensible thing to do. That said, the full-size cover images in the KF8 files I have unpacked to EPUB are manifested, but not explicitly indicated as being a cover in the OPF. I suggest adding a name=”cover” meta tag (as per Amazon) and/or cover-image property (as per EPUB-3).
ETA: Ooops, my bad.. The cover meta tag IS present in the unpacked files. Never mind.