In this case, a single-file solution is fine. On my Mac, I have a Dropbox folder with Markdown files, one per scene (one directory per story). I use Brackets to edit on the Mac, and Jekyll to build HTML files for previewing or building EPUB (eBook) files. I have some custom scripts to transform a validated EPUB into PDF for drafts, or typesetter markup for PoD. In some ways, it works better than Scrivener—except, right now, for editing remotely on my iPad. I might give Byword a shot.