Assuming a physical-only universe, presented with a phenomenon that doesn't seem explainable from within that worldview, we downplay or otherwise explain away the aspects that don't fit in. The assumption is that *everything* has to be explained, everything has to have a physical cause and effect explanation.
The mature spiritual worldview instead expects that there will be phenomena that can't fit within the finite explanatory framework that we are within. Not frustrated by the requirement that everything has to fit within the arbitrarily bounded worldview we're capable of, we can play within the universe. We know that further explanations may arise in time, but we're not less because we don't know everything.