calibre does the best it can based on the heuristics of the book.
Unfortunately most ebooks define scenebreaks via a CSS class for regular paragraphs and a separate CSS class for paragraphs with a preceding/following scenebreak, and set different top margins depending.
calibre cannot deduce the meaning there, though if you invent a working Artificial Intelligence Kovid will happily include it to do just that -- also you will make billions in consumer tech.
Proper scenebreaks would use their own paragraph containing
at least IMNSHO

but definitely something more semantically meaningful than the current popular convention.