Well, as far as I've heard, Calibre doesn't support EPUB3 creation (yet?), so you're limited to XHTML 1.1 of EPUB2. Even if Calibre supports EPUB3 in the future, if you don't disable EPUB2 creation, you have to comply with XHTML 1.1 of EPUB2.
I find your position quite scary, because there's more software that works with EPUB files than just e-reading devices, and you deliberately break them by producing invalid EPUB files. So I don't wonder anymore why users of Calibre frequently run into problems when they try to use their Calibre files in serious processing software or services.
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The only reason epub validation exists at all is because, it is, quite literally, the simplest thing to program a tool that check HTML against a DTD and pops up lots of meaningless errors, as opposed to writing a tool that intelligently checks the HTML for things that are known to be problematic in real world usage.
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I don't know if EPUB validation is usually done with DTD or XML Schema validation, but the latter is standard for all kinds of XML formats, and therefore will be (if it isn't already) used to validate EPUBs too, so you'll never escape checks for EPUB standard compatibility on files Calibre produces. Regarding your explanation, it seems you want to check for all kinds of more complex errors, but introduce simple errors yourself.