If we hand out "advantages" based on grappling pedigrees, then yes, Werdum had a significant one over Nog. However, this is MMA--not ADCC or the Mundials--and Nogueira managed to hang with Werdum on the ground.
Pedigree can indicate a lot, but honestly it's not a definitive way of looking at who will have the edge on the ground. Look at UFC 85 for instance:
Kevin Burns--a recent blue belt in BJJ--submitted Roan Carneiro--a world-class BJJ champion--with a triangle-choke. No one saw that coming, but it goes to show that MMA-BJJ and standard BJJ are not synonymous in the least.