This is because when the reference points get added to Navisworks their origin will be at 0,0,0.
If the reference points are far away from your model then move your model to the reference points rather than moving the reference points to your model.The reference points plane will now be selected, use the Transform tools under the Item Tools to move and rotate the reference points to your desired location.The Selection Tree will appear to the left, navigate to and select the desired RedCraterReferencePointNavisworks.nwd, it should be at the top of the heirarchy.
Navisworks model Exporting from Navisworks: