Would be nice if our DSSSL/XSLT experts would comment on what does a change in the DTD (to accept child pages in reference) or the used tag (to be able to break the reference) mean in the end. You might be able to try on a simple prototype. Question is what effect would it have on the TOC and generally on the display of that reference section, if you would change it to use <chapter>.
I changed mysqli a little bit (<reference> to <chapter> and <section> to
<sect1>. For an example see http://www.php-award.net/mysqli/index.html
This does not seem to be that bad :) I wonder what were the good points on using reference instead of chapter here... Chapter seems to be able to contain a <refentry> just fine:
http://docbook.org/tdg/en/html/chapter.html
Would be nice to validate your resulting XML against the used docbook version's DTD.
Goba