Found via a blog post by Adam Tinworth: The publisher of The Magazine ran a Kickstarter project to put together a hardcover book and e-book of the best of The Magazine’s first year. When it came to producing the print book and the PDF, the going was easy.
But they found converting it to EPUB considerably harder, because whereas PDF is concerned about replicating the print format precisely, EPUB must by necessity be more free-form. Which meant effectively having to undo all the fancy formatting they did for the PDF version. Said publisher and his helpers consulted with many experts on the various means of producing an EPUB, but couldn’t find any easy solution. “[They] all have their own zigs and zags.” It ended up taking them weeks of work to produce something halfway decent.
Going by this article, it seems as if the tools for simultaneously publishing PDF and EPUB professionally—at least for people who aren’t part of big publishing houses which presumably have custom-built, specialized tools to help with that—just aren’t “there” yet. Will they ever be? Or are the processes destined to remain just too different for easy cross-compatibility? It’s an intriguing question, and one that I suspect will be with us for a while.