No, it won't break anything, the ibox transitions may not look quite as groovy. iBox is used for the help links and for the image gallery.
opacity while not valid css does work in all major browsers.
Nevertheless, I agree it would be better to have it pass the validator, its not really a major difference even in ibox.
I will make the same css changes here so it will be corrected in the next release.
I recommend re-enable minify and caching of css.