Thanks Kovid, appreciate the response, and I really appreciate all the work you've put into Calibre - it's a great tool and it's really enhanced my ebook experience for years.
I did do a little more experimentation and I found I was able to strike a kind of balance, converting to em values I managed to get the formatting more or less how I desired, but I'm not sure if that will work on future books I convert.
Are there any profiles in calibre which prevent the px-pts conversion? ideally I'd like to retain the original styles as much as possible, though I am aware that might be difficult to do when the ebook is being converted from one format to another - I don't even know if mobi support px values, to be honest.
I tried using AZW3 but when I did that, the nested ToC in the book only went to the second level on my kindle, so unfortunately that's not an option either.
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