alt Hacker Newsepubcheck is meant to ensure conformance with the standards, not the interoperably implemented subset of the standards. (Which has lots of awkward questions: which implementations of the standards, which versions of those implementations, etc.)
epubcheck is meant to ensure conformance with the standards, not the interoperably implemented subset of the standards. (Which has lots of awkward questions: which implementations of the standards, which versions of those implementations, etc.)
The latter seems like what the tool's users actually want. That it's a harder problem doesn't change that.