Implemented the second option for reference linking, and got it all working. Briefly:

• When the XQuery retrieves a document from the db, it checks for <ref type="reference"> tags. If it finds any, it creates a <back> element containing a <div type="references"> element.
• For each ref link it finds in the document, it retrieves the matching reference <div> from the references subcollection and puts it into the <div> above. This means the XML document now has a matching explanatory text for each unique reference in its back matter.
• The XSLT then detects the presence of these, and turns each <ref> tag into a link which calls some JavaScript.
• The JavaScript pops up the reference information on the right of the screen.

The display of reference info looks very similar to that of note info, but it's not; the notes are displayed through pure CSS using :target, but the references cannot be set to position: fixed because they're frequently very long and need to scroll, so they're set to position: absolute and just placed next to the calling reference link.