Since the editor doesn't recognize EPUB3 and aparently EPUB3 doesn't recognize doctypes, what is the problem?
(Did EPUB2 recognize them?

)
Wouldn't be the first time missing doctypes irritated calibre users, and calibre still doesn't care.
They are unnecessary and their only purpose is basically as a security blanket, so... ignore them?
That was the general idea in EPUB2 as well!
Honestly I don't quite understand what this has to do with EPUB
3 specifically anyway, can we file this under "calibre eats my doctypes and I like them so please hands off"?