It has to do with the fact that there is a metaphysical part of the universe. There is something bigger and deeper than just the material. And yes I believe it is perspective and because your perspective is limiting your vision to the idea that something can have a metaphysical or spiritual component is the issue. I do not think that there is any reason that science and the metaphysical do not work in concert together.
I, too, think that metaphysics can be part of science fiction. After all, 'metaphysical' and 'spiritual' just denote concepts that haven't been described scientifically yet. Everything is explainable, it just requires enough knowledge, time and technology to be understood.