The command line option and the gui option do not mean the same thing, apparently:
https://bugs.launchpad.net/calibre/+bug/1255541
I solved this by including extra_css = 'p {text-align:justify}' in my recipe, but it is a bit ugly as somehow who prefers other justification would have to hand-edito the recipe. It would also not work if the source did not have all text in p tags.