For exporting documents so they look the same everywhere, I wholeheartedly recommend PDF. It looks the same on your (the author's) computer as it will on their (the publisher's) computer. However, producing that PDF may be tricky, and quite possibly unnecessary.

Are the authors fully in control of layout etc? Here's what I'm inferring: you're building a site to allow/help authors write/store some documents of some sort (books; reports; whatever). These authors will decide what layout etc they want for their document, they'll "export" this, and send the exported version to the publisher. Are my inferences correct?

If they are, I'd recommend seriously considering RTF and restricting the authors' options for layout etc — authors are there to produce content, typesetters are there to decide layout. Very few authors (I can only think of one) are actually good at laying stuff out, therefore your system should (IMHO) allow them to create the logical (thought) structure of their documents, and the publisher will bugger about endlessly with the layout.