A somewhat tricky issue. If I use export_raw, it’s sufficiently easier to reformat pages in the layout script, than it is to have nice looking automatically numbered references via RefNotes in the DokuWiki view.
What seals the deal is twofold; you cannot click on the note markers in the reader on DokuWiki, and, the named note has to have the same name as the note in the Notes section. So from the standpoint of editing the documents, using RefNotes is an overhead without much benefit. It would be easier to just use square brackets and, if push comes to shove, write a small plugin for DokuWiki to render internal links with single square brackets. Plus what sucks is DokuWiki’s RefNotes cannot handle notes which begin with a number! Alas, it would have been great if it worked. But it kinda does and (mainly) kinda doesn’t.
And the fact is, the DokuWiki version is really just intended to maintain the documents in the first place.
The layout manager is intelligent enough to do the linking for itself anyways.