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Calibre doesn't have any logic to sort out one vendor's epub rendering quirks vs. another's.
In general an epub that comforms to Flightcheck in Sigil or epubcheck will render just fine across all epub readers. What you may see is slightly different interpretations of the spec on some readers and slight differences in rendering, that's it. Most epub readers actually use ADE's engine, which means in general they render identically.
There are some egregious oversights/extensions on some vendor's parts, like Apple's including of video, fixed width proprietary extensions, and ignoring of standard font embedding/handling practices. Calibre doesn't try to fix any of that for you automatically though.
The only thing you need to convert for in general is for readers which don't support epub, e.g. mobi for Kindle.
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