Maybe it isn't YOU who's aiming to publish it in the Kindle Store? You can let Amazon run it through Kindlegen on their computers, or you can run it through Kindlegen (probably by simply dropping it on Kindle Previewer) locally. Then it's a good idea to try it on your computer's Kindle Reader application. It's hard to get a preview of how a conversion will look on the iPad Kindle reader unless you own an iPad.
If you've never created an epub that passed EpubCheck but caused errors in Kindlegen, you haven't be trying hard enough! Not to mention one that's "legal", but doesn't view as expected in Kindle.
Nothing's perfect. But I strongly warn against falling in love with one particular set of tools :-)
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