If it checks for the models in the folder(it does not create mdls), then instancing is easy as it'd just place a model for every object of the same name in the scene. If it can make .mdl models as well(which would be awesome), then it might be more tricky, as it'd have to take only one object of the same name, export it's model, then place that model for all the rest of the objects in the fbx scene with same name. Either way, any objects in the fbx scene with the same name should be instanced. But yeah, would have to try it out before too much discussion.