Yeah... alloys are funny things. Sure, on a nuclear level there would be copper nuclei interspersed with aluminum nuclei, but they form distinct phases that have physical properties often significantly different than either pure metal. In allomancy at least, it would seem that the alloyed metal is treated as a separate metal, which would imply that the atomic level isn't what drives the metal properties. Or perhaps that Brandon isn't a materials scientist, but a (rather good) author. One of those two.