I do think there are things in the "mystical" world that are not yet explained by science. And not because these things are unexplainable in their nature, but because they just haven't been fully studied yet. And because a lot of consciousness type things are basically only yours to experience, so it's impossible to really "study" and observe. Taking drugs as an example, you do see consistant biological changes associated to certain substances. And you can measure heart rate, do fMRIs and measure electrical activity. Or ask a person about how they feel and conduct tests. But that doesn't mean you can see what they are seeing that moment or feeling what they are feeling.
Similarly, I think a lot of religious rituals have created frameworks and techniques that can reliably achieve certain results. Stuff like kundalini meditation and chakras seems like a bunch of spiritual mumbo jumbo at first, but it's been around thousands of years. Anyone that does these exercises, even for a really short period of time can feel some strange sensations in their body. And I've actually heard accounts of people doing those exercises, triggering some irreversible process and going trough literal hell with physical symptoms for YEARS. Stuff like extreme chronic pain and insomnia that doctors could not help with. But apparently though work with Gurus, people have resolved their issues. It doesn't mean that the beliefs behind those practices are true, but that a lot is still unexplained by science. And that going through the motions of an age old practice when there is no alternative, can actually mysteriously help.
With all the belief I have in modern science (and being the successful recipient of a brain surgery that cured my epilepsy that would have been impossible 30 years ago), I think matters of the mind are an area we really don't know much about. And everyone is so individually different, with different chemistry, life experiences and circumstances. Even the troubles we can identify (depression, adhd, ptsd, addiction), we often can't cure or manage successfully. We're getting better every year, with new therapies and medication, but we're far from success. So I see no harm in therapies that seem weird or without scientific explanation if they do work.