Maybe that's true, but even then, the biological activity from the brain could be an effect from the spiritual experience, and not just the cause of the spiritual experience.
"Imagine that I look at a dog. Visual information from the dog passes through my eye and my optic nerve to be processed in the brain. If you SPECT-scanned my brain while I was looking, you would see lots of activity in the visual processing areas. Has that activity caused the dog? Of course not, although it correlates perfectly with my dog-viewing. Does the fact of the observed brain activity mean that the dog is a delusion? Of course not. All this is almost too embarrassingly obvious to say, and yet it is often suggested, on analytically identical grounds, that we can confidently say that there is a 'God Delusion'."
-- Source: Wired for God? The Biology of the Spiritual Experience; Charles Foster
It depends on how specific they get. Different substances or practices affect the brain differently, but it gets a bit more specific than that example.
For example, in many spiritual or meditative or prayer experiences, people report a feeling that space and time is altered or doesn't exist. But when it turns out that during those experiences, their frontal lobe (associated with concentration) is increased, and their parietal lobe (associated with the ability to internally organize surroundings in space and time) is greatly increased, then we've got something there. And when there's another study showing that people with injuries to their parietal lobe are more likely to report spiritual experiences, we've got another thing there. Plus it's combined with observation of the general medical problem that certain types of parietal lobe injuries cause problematic symptoms related to, among other things, spatial perception.
So using just that specific example of the parietal lobe, if it can be showed that a) the parietal lobe doesn't just observe spatial activity but plays an important role in organizing it, and b) doing certain things, like intensely concentrating on something, results in increased activity in the frontal lobe and decreased activity of the parietal lobe, and c) participants then report experiences of altered or absent spacetime recognition, then there's more than just an argument of correlation there.
It's quite different from being unclear about whether visual activity causes the dog or whether the dog causes visual activity.
The last part of the quote is problematic because it's linking the title of a book that has little to do with this topic, to the topic, probably to score emotive points.
If anything, demonstrating the science and causality behind those types of experience is helpful to the practitioners rather than harmful to them, because it reinforces the notion of how it works and what it's doing. The first time I ever tried meditation was after reading a set of scientific studies on it showing that there are measurable brain responses going on and that even in a secular context it's a potentially useful exercise. Plus it can be argued that if the parietal lobe is basically an organizing filter for interpreting our environment, then decreasing activity there results in a truer interpretation of the environment rather than a delusional one.