I have a AT and only used the new maps so i have no frame of reference. I can understand why it would be an issue on a 6 sp but in the end it can be all tuned out so i see no reason to change the tuning tool aka Cobb.
Cobb tuning for this car is still in its infancy, more tunes with better refinement will be out soon. Its fun making incremental changes. Hold on and good things will come your way
Harry