Another way they could do it is have it as a complete xx amount of FATEs to obtain the atma, they could tie that into lore by saying something like once so many mobs have been defeated (but we would still use FATEs) the aether released by the slewen monsters would react with the Zenith and crystalise forming a type of crystal known as Atma. Also to tie seperate zones into lore they could say "the environment inwhich the aether crystalises seems to affect the type of Atma created."