Calibre puts
<dc:identifier opf:scheme="ISBN">
and
<dc:identifier id="uuid_id" opf:scheme="uuid">
into content.opf. It also includes the entry
<package xmlns="http://www.idpf.org/2007/opf" version="2.0" unique-identifier="uuid_id">
which if I understand correctly, is telling epub clients that the uuid is indeed a unique ID. This is what I want, because I actively remove ISBNs, making them useless as an ID (for me).