At the end of the Freelancer story the Hypergate in the Inner Dyson Sphere is activated. But when I go there in CF i find the hypergate to be sadly, gone. The CF story says that X3043 was the major system of Nomad Activity. So if thats true than maybe the nomad gate in Inner Dyson that leads to X3043 should be replaced with the Hypergate.
It just makes more sense storywise.