You are providing an excellent recommendation in ensuring that the Hard Drive is De-Fragmented and the Temporary Directory where CloneDVD is processing DVD Files is also Un-Fragmented.
You imply that this is only pertinent if you are burning to Dual Layer DVD Media. It should be noted that this recommendation applies to all instances even if you are burning to Single and/or Dual Layer DVD Media. This is just good prudent computer management and has nothing to do with Dual Layer DVD Media.
You also imply that it is prudent NOT to update to the newest most recent versions of CloneDVD and/or AnyDVD. In the volatile ever-changing Commercial DVD Movie Titles copy protection arena this suggestion only leads to definite and well-documented problems. Suggest visiting the SlySoft AnyDVD history change log (http://www.slysoft.com/download/changes_anydvd.txt) and SlySoft CloneDVD history change log (http://www.slysoft.com/download/changes_clonedvd.txt). In reviewing these change logs you will see that SlySoft has expended great efforts to update and improve their software programs to deal with the new technology employed by the Commercial DVD Movie Titles manufactures. Suggesting not to take advantage of their efforts and expertise is questionable.