I think they are both the same. If you are going to upgrade to 64gb Ram then you would go for the single 16gb chip... since the max amount of ram per slot is 16.
Getting the 16gb one is good if you were planning to add more ram in the future... it free's up more slots. We use iMacs at work, and the memory is at 32gb, but all four slots are taken up with 8gb sticks.. so if we ever wanted to upgrade to 40gb or a higher number... we would have to remove one of the memory chips.
I don't know why apple didn't put two 16gb chips in it...