It's simple, no one cares enough about EPUB 3 to develop any tools for it. It's a solution looking for a problem.
As for your confusion about <dc:identifier>
Code:
<dc:identifier opf:scheme="calibre" id="pub-id">whatever</dc:identifier>
is valid in EPUB 2, but, it is not valid in EPUB 3
In EPUB 3 it needs to be replaced by this
Code:
<dc:identifier id="pub-id">whatever</dc:identifier>
<meta refines="#pub-id" property="identifier-type" scheme="calibre">calibre</meta>
or if you dont care about the scheme part, just
Code:
<dc:identifier id="pub-id">whatever</dc:identifier>
calibre only knows about EPUB 2 so it will always generate <dc:identifier> elements with the scheme attribute.
If you dont want it to do that, go to the editor preferences, and under calibre integration turn off automatic metadata update.
So, the executive summary for people that would rather not understand:
1) Turn off automatic metadata update under calibre integration in the editor preferences
2) Remove the scheme attribute from all <dc:identifier> tags
3) Give yourself a gold star, epubcheck now approves of you, and no one else cares