Toxaris is right here: if you put the PDF inside the container, you can link to it via a relative URI. However, good luck with having it working.
It is the same problem I am running in the EPUB3 Audio-eBooks my company is producing: we put in the container an M3U playlist, hoping that someday, some Reading System will support it, e.g. letting the user choose between "listen only" and "read + listen" modes.
The same applies to your embedded PDF: maybe some day RS will "realize" that the link points to a PDF, and suitably render it.
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