I thought the atoms were to boost your stakers i you didn't have enough coins for a master node? Why wouldn't someone with 100k ions need so many atoms?
My guess is those IONs are locked into stakers because they have been converted from XPY (so can't be withdrawn to make masternodes), and those atoms have been converted from XPYBits, which had a different purpose before xpy.io was rebranded into ionomy.
Also stakers "guarantee" a certain APY whereas masternode's revenue depends on how many other masternodes are on the network, although that's a whole other story.