In our current system we have tags with ids called ein numbers - <story id="0123456789">This Story</story>

When this story tag gets placed on a page the ein number and the page number gets put into a file.

Other tools can use the files to reference the story and create links to the document and the spot where the story begins.

We also build our TOC's which are not in the same document using these files and they are used in our search systems.

You could access the page numbers in Prince using JavaScript that runs after typesetting and then logs the information using the box tracking API.