I don't think so, there is a slight difference, but not much. Like how you said, it's if asking someone "are the pieces of cake small?" or "are there small amounts?", one is asking if all the pieces are small or if there are any small amounts, which is like saying that you'll take any one that is small. Hope you understood that.
It's a matter of context, not of specific adjectives. Here, we have a question and the emphasis falls on "mici". The noun-adjective order switch also takes place in English:
Those are the small quantities. - Acelea sunt cantitățile mici.
Are the quantities small? - Sunt mici cantitățile?
Note that "Sunt cantitățile mici?" is also a valid question, but, for me, it has a different nuance and I don't feel qualified enough to try to explain.