I am not quite sure what you are saying?
The fb2 output currently has
<a id="calibre_link-2"/><strong><p>CHAPTER 1</p></strong><p>
.......
</p><a id="calibre_link-3"/><strong><p>CHAPTER 2</p></strong><p> etc
What is wrong with creating it like:
</section>
<section><title><a id="calibre_link-2"/><strong><p>CHAPTER 1</p></strong></title><p>
.......
</p></section>
<section><title><a id="calibre_link-3"/><strong><p>CHAPTER 2</p></strong></title><p>
etc.
This gives the page break at each chapter and also splits into fb2 sections.
The title is whatever is found by Calibre, at worst you will end up with the odd extra chapter/title that may be picked up by mistake but that would be much better than no chapters/titles.
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