The Caput Mortuum seemed to take the longest for me whereas the yellow gummies (I think its Orpiment?) I had in spades.
I did pretty much all of my Atma farming in OC until I went to farm fates with an FC mate.
Based on our experiences, I would definitely say that OC has better drop rates for Atma than farming fates in DT zones; we were farming her last set for like 6 hours over the weekend before any dropped.
Its easier to make it to the fates in the overworld though since they just get deleted in OC, so I guess you have a choice between convenience and a higher drop rate.