I've owned AnyDVD, CloneDVD and CloneCD since 2003 and I've been a Nero user since before that. If I have Nero anyway why not make use of Nero Recode? As an existing Nero customer I get upgrade discounts for newer releases, etc. So, yes, it does cost money but for me it equates to better results. If a person wants to they can use Shrink which is just a freeware ancestor of Recode.
But, in the end, the answer is that sometimes CloneDVD and AnyDVD aren't the best by themselves. For ripping and burning dual layer DVDs then there's no need for Shrink or Recode at all so that would make the issue moot. Personally, I always rip and burn to single layer discs while removing what I don't need.