First, I do not think that locating the causes of the experience in the brain excludes psychosis from being a spiritual experience. To me, the spirituality of the experience has to do with the content, the meaning of the experience, not with its causes. This content is not determined by these causes. I can very easily grasp the meaning of some phenomenon without knowing how it came about. I do not need to know how someone died to know what his death means to me. Similarly, I know very well what it means to experience paranoia, the hostile world you encounter, everyone seeming to plot against you etc. This I know without knowing how it all comes about, there is ofcourse correlation with neurotransmitters and maybe inflammatory stress etc. But I do not know the mechanisms through which such phenomena result in the experience of paranoia.
As for the spiritual part, like I said, this has to do with the contents of the experiences. To me, psychosis seems very much a breakdown of what was always taken for granted. Your identity, the way you experience thought as private, as yours. The reality of the external world… These are issues I normally do not even notice, but would confirm if pointed out to me - I do not experience them as put into question usually. These are tacit givens that constitute the world as I normally experience it, rather than that they are present in it as particular noticeable experiences. Normally, i do not so much notice the reality of the world, but in psychosis it becomes an issue for me. Similar to my identity. It is unusual to experience myself as being such and such, yet of course, it influences what I experience and how, like how people react to me. So what was ordinarily taken for granted, what ordinarily formed the context of experience now, in psychosis, takes centre stage. In this sense, it is metaphysical, and can be called spiritual.