It doesn't make much sense to me from a story standpoint. I find it pretty hard to believe that Xemnas had no idea that Marluxia was going to turn out to be a traitor. Why would he knowingly leave his second facility in the hands of a traitor? Even if he WASN'T going to betray the organization, there were still plenty of other people more deserving of the job. Marluxia was #11, one of the newest members of the organization. Why wouldn't he leave it with Vexen, #4 and someone he actually knew when they were both somebodies?