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This isn't a bug - these scene breaks are set using CSS, as you noted, and you enabled the 'remove spacing between paragraphs' option. That feature is essentially a giant hammer which zeroes all the css relating to paragraph spacing (as it's documented to do). Just disable that feature and use Tweak ePub or Sigil to manually edit the css after conversion to eliminate the spacing between normal paragraphs (calibre119 in your example).
Heuristics can't help here, it's looking for other types of scene break data that often gets screwed up from other conversion processes, but it doesn't check css.
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