I just found that when I add Project Gutenberg EPUB3 ebooks I don't get their identifier in Calibre, despite them being included as dc:identifier property in content.opf.
However when I add the EPUB format, URI identifier shows up as expected.
Example:
https://www.gutenberg.org/ebooks/74324
epub 2 has
<dc:identifier
opf:scheme="URI" id="id">http://www.gutenberg.org/74324</dc:identifier>
epub 3 has
<dc:identifier id="id">http://www.gutenberg.org/74324</dc:identifier>
Well I just unpacked the EPUB3, copied that EPUB2 line into the EPUB3's content.opf, and Calibre has set the identifier, so I guess that's something related to the missing opf:scheme="URI" bit.