Relative links in an EPUB refer to files inside the *.epub, relative to the currently rendered resource (the (X)HTML file containing the link).
You'd have to embed the PDF or whatever as a Miscellaneous file inside the EPUB, and then I doubt any reader would open it.
file:// links point to locations in the filesystem hierarchy, rather than being interpreted within the renderer's context (context can be anything. A file://page is a filesystem context. a
http://website.com/page is a website context. Relative links in either case are relative to the
currently rendered file.)
If you use a file:// link, it will escape the EPUB context. There should be some way of munging that to use a relative link...
It *might* work, but I don't guarantee even if it does, that it will everywhere. As far as the specs are concerned, you are most likely a filthy troublemaker.
Enough reader applications rewrite the wheel that they might be doing anything.
