never mind not being able to add the books to online marketplaces (such as Amazon) because, again, the output does not validate.
I think the simplest thing to do would be to update the wiki and have a note that informs readers that while ConTeXt can be used to generate an EPUB, it is likely that that EPUB will be unusable for devices without further transformation of the XML content. At least that way the knowledge is out there and people are forewarned that not all EPUB documents are equivalent.