Having spent a regrettably large amount of time on forums where the 'magisteria' type questions were had, I think that you're representing the 'outside of science' position slightly unfairly. Obviously, it often tries to have its cake and eat it. But you're substituting 'standard rationality', or perhaps 'questions of cause and effect' for 'science'. Some magisteria-types would say that there are direct causal effects from God or ghosts, but that these do not manifest with the regularity of things that you're likely to be able to find through scientific experiment. They think that the world is better explained by including God or ghosts, but that you can't devise an experiment to prove/disprove them (for a variety of reasons, up to and including 'the ghosts don't come out when you're trying to test if they exist'.

This is aside from the people who basically mean that their religion or whatever is just subjective.