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 standard exists, it is the responsibility of both the producer and consumer of ePUB files to adhere to the standard.
Though these days I have to spend more time worrying about EAA and ADA compliance than anything else.