Good question, normally I just use alt-d to duplicate a object rather than shift-d, alt-d making it a instance, however I am fairly sure this is just rote and there is a more formal way to make a object a instance. I admit I find instancing of objects in blender a bit of a black box. That being said luxblend seems to do a very good job of honoring instances defined in blender and I have personally never run into a case where luxblend missed anything.
Btw, I forgot to add in my prior post that this render is inspiring in the sense that I think we should have a pure space-ship render comp. It seems like it would be a lot of fun to try a space ship render. 