I dont see what's so hacky about it. But if you really want to run just the cover generator, do it like this.
Code:
calibre-debug -c "from calibre.ebooks.covers import *; open('cover.jpg', 'wb').write(create_cover('my title', ['my author'])))"
And you can set whatever preferences you like when using the create_cover function, see the sourcecode for details.
As for EPUB 3 sure someday, but since the EPUB standards are a bad joke and there is nothing you can do in EPUB 3 that you cant do in EPUB 2 I'm not particularly motivated to do so.