First, it is not easy to make a print like pdf out of an ebook. Maybe if you use latex you come close, but I won't say this is easy. If all you want is hyphenation and justified text, then there is a calibre plugin for that.
For multi-level toc, at least kobo does not support this also (i miss it too). A workaround could be to let calibre make an inline-toc. But of course, that would always be one click more.
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