For the purposes of this questtion, let me spell the English word "atopy" as "atopia". I have no idea why the the same kind of etymological background (same derivative on the same Greek word τόπος) has lead to two different endings in English, but that is not what I want to ask here. In many other languages these two words seem to have the same spelling (at the end).
Utopia means an unrealistically perfect place, and the word means roughly "non-place". Atopia is a condition that is not localized in any particular part of the body, and the word means roughly "placelessness". I want to compare the prefixes u- and a- here.
From the point of view of classical Greek, how do the prefixes u- and a- compare? Would they correspond reasonably to the use in "utopia" and "atopia"? Was u- even ever used as a prefix like this in classical or older Greek, or is the derivation a more modern invention?