The primary difference between using KindleUnpack vs. calibre conversion is that calibre will flatten the CSS. Oh, and also for performing scientifically-minded analysis of the format.
If you don't know what that means, it is a sign that you shouldn't care. I personally would not bother mentioning KindleUnpack to anyone who isn't exploring mobipocket internals, but some people have a bug about the "impurity" of converting.
(odamizu, I am unaware of you holding those kinds of opinions
but you reminded me of someone who does get into a snit about this.)