You are correct regarding the missing rear audio channel on episodes 1 and 2 of the PS3AVCHD Presents releases and I agree, it is an irritation.
But, I don't believe that the proper 12GB Wookie Groomer transfers have this fault - I don't recall it last time I watched them. Are you certain that PS3AVCHD used Wookie's transfers as their source material? If you look at Adywan's AVCHD thread, he's working on HD transfers in this format too but he's not using Wookie's work as source.