This is a key understanding here. What we model reality to be, which we then act upon, is in fact us interacting with our metaphors to describe reality. You said it right there, "It is best to act as if it is real". As-if statements are metaphors. Naturalism, is a metaphor, just as much as theism is.
When you assume that how you think about reality defines what reality is in itself, you are making the same error of thinking as those before you historically who imagined as they looked up at the night sky that gods were up there. They interacted with it "as if" it were real, and it served a true and genuine model of reality for them to operate within. You look up at the night sky at the tent you see, the model of reality you superimpose upon it, is a scientific one. You imagine that the "evidence" we have that supports our models actually defines it's genuine and true nature, just as the ancients saw gods. They had their supports as well.
It's all metaphor. It's all "as if" it were reality. And as such, when they function for those who use that language, they are valid, even if less or more useful depending on the requirements.
What you perceive in reality in fact will be limited by the models of reality you use and engage with. As an example, if you don't know how to see a "ghost" because you've never encountered one, if you saw one your mind would not allow it because there is no mental model of one you could associate it with. What your mind would see might be "an old woman", or something it could try to connect it with. So, to others where that was part of their mental 'vocabulary', they would see it.
In other words, even if you were looking straight at it, you might not see it because your mind disallowed it.
If you have an experience that does not fit your current mental models of truth and reality, that becomes a reason to explore beyond them.
