Epigraphs are generally meant to be part of the story or a mood-setting lead-in (if fiction), and some of them are quite important. I have a set of old Robotech novelizations where every single chapter is preceded by an epigraph of fake quotes from made-up books, interviews, and other materials done "in-universe", and they really add to the world-building.
I'd just have the chapters in the TOC go as usual, but have the chapter nav link go to the appropriate epigraph which starts the section, and use a page-break if necessary to set the following narrative text off.
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