If a model is in RAS coordinate system and the coordinate system is not stored in the files then you need to select “RAS” when you load it (in “Add data” window). When you save this model, it will be saved in RAS coordinate system (to cause minimal change in the file), but the coordinate system will be stored in it. If you want to save as LPS then you need to change the coordinate system in its storage node:
getNode('SomeNode').GetStorageNode().SetCoordinateSystem(slicer.vtkMRMLStorageNode.CoordinateSystemLPS)