There are not a huge number of ePubs from commercial sources without DRM, but those that do exist provide a relatively wide range of ePub styles for testing. I looked at some of them from a chapter heading viewpoint in
Ebook page design. So I tried using any2mobi (default settings) on these examples. About half failed, and I'll post bug reports on calibre trac. One surprise was that all three FeedBooks ePubs I tried failed to work. FeedBooks has its own MOBI option, but we should still be able to convert their ePub to MOBI.
The attached screenshots are from the original ePub (Adobe Digital Editions) and the any2mobi MOBI (Windows MobiPocket Reader).
Appleton's Alice's Adventures is from Adobe's free library. It works well except for color in the chapter header and quotation marks and other special characters which are not displayed correctly (wrong encoding?). MobiPocket isn't capable of wrapping text round an image, so that lack isn't any2mobi's fault.
One of the two Penguin samples I tried failed, the other worked very well except for indenting the start of paragraphs. Penguin's have embedded fonts, which are not being transfered. So far as I can tell, the ebook is just using the reader selected font (Times New Roman).
Rosetta's Red Alert is also in Adobe's free library. Its chapter header isn't transfering well, but the rest looks good except for the indenting of the 1st paragraph.
The threepress Huck Finn again has paragraph indent issues.