This is predicated on T49544 not being fixed, appetite for which seem minimal.

Currently, the references are in a <li>, and each reference is a <span>. This doesn't work very well when there are block elements like <p> and <div>, because nesting a block element in a span is a sin.

For example the attached EPUB goes badly wrong in Koreader. Changing the <span> to a <div> fixes it.