What you are attempting is rather complex
I get the sense you want to portray a "belief in spirits" in that exists in your world, without expressly
compelling the reader to believe in their existence as veridical; but without, on the other hand, pushing some form of 'atheism' onto the reader by implying that all metaphysical concepts should be unquestioningly dismissed as a matter of human reflex?
I think the answer to this lies in Aldous Huxley's non-fiction works,
the doors of perception and
heaven and hell.
In these he describes a kind of "spiritual world" that perpetually exists within side one's brain, as a function of the unconscious mind. He then goes on to describe the theism/atheism split, largely in terms of a failure of one party to perceive this world in of itself (and hence the use of psychedelic drugs to open it up) but then also as a difference of category: The Theist would view it as a world that transcends and supersedes our own; while the Atheist who manages to see it, would then use science to categorise it as something that exists purely as a subset of the Physical.
If you want to layer the metaphor for "spirit" in such a way that you don't twist the readers arm... I suspect the answer will be in describing it at a level of complexity, somewhere along these lines. The reader could each take their
own view of the situation without feeling pressured to see the world at large from a philosophical perspective that challenges them: you are essentially describing both truths at once, nested within the one higher meta-truth.
As I said, very difficult. Huxley did it, but he took a hell of a lot of drugs to get there.