Is it possible that these rocks were like prehistoric coffee tables, and the cavemen hadn't yet invented coasters, and their hot drinks had slowly worn these "cup" maks into the stone over the years? Makes you think, dunnit? Eh? ;o)
This actually backs up my theory that Maen-y-Bardd is nothing to do with poets, but is a pervesion of Maen-y-Bord, which would mean something like 'stone of the table'.