Calibre has no idea those spaces are supposed to be scene breaks - it's just a margin. That's one of the issues with ebook design IMHO - traditional HTML design methodologies dictate all layout should be controlled by CSS. This makes sense for Web, but it doesn't really make sense for ebooks - there is no such thing as a 'lossless' ebook conversion, so it's incredibly easy to lose information that is solely defined in css. That's why I define scene breaks as an empty paragraph <p> </p>. Traditional html design says it's a no-no, but this information can't be erased when format-shifting ebooks.
The other issue is the thing that you're asking for, while it would certainly be nice, would be quite difficult to implement. Aside from the heuristics features, Calibre never 'guesses' anything. You'd essentially have to create a heuristic scan across all the css styles in the book AND their usage in the actual text to guess which one(s) might be a scene breaks, and then you'd have to be smart enough to somehow over-ride all the settings that Calibre provides to directly manipulate css. And then of course you'd have to deal with the support nightmare of directly conflicting features and users who don't understand them and leave them all enabled.
You will also find that not all of your ebooks use css - many ebook creators recognize the conundrum I mentioned above and also use empty paragraphs to define scene breaks. The fact that many editors follow that practice means you don't always need to worry about this issue, and it also makes it not really worth the effort for any developer to even consider developing/supporting some sort of heuristic.