If it did not happen in the mind, where else would it be happening? Your statement probably came out a little bit wrong, and I think what you're really trying to say is that these experiences have no validity(?). If that is the case this is your assumption and an assumption only, because there is nothing that really indicates that this is a fact. Sure, you can choose to explain a transcendental experience through neuroscience, but what does it matter? It gives us a clue to what is happening within the brain, but it does not explain the experience itself - the experience is still there, and it happened THROUGH your mind in the same way EVERYTHING in your life flows into the mind where it becomes an experience for you.
You can choose to explain all kinds of experiences through this framework, but the experiences are still there Burnt. And how organized matter creates an experience of what we call reality in the first place is a question too big to really answer, at least for now. And what scientific law in the whole universe says that our normal setup of chemicals in the body is the only true way to perceive reality? Who says that an altered chemistry in the body creates false experiences and false experiences only?
Our body is in the shape it is in to best deal with the challenges of our environment, it's pretty obvious we don't perceive everything that is going on around us at all times. All species perceive their little corner of reality with their bodies and its own set of chemistry, we are no exception. And within a specie there is a whole lot of different individual creatures experiencing reality a little different from everyone else in the horde. It would for example be IMPOSSIBLE to imagine how a little fly experiences reality, or a cat, or a dog, or whatever. Even another human being for that matter. So claiming that an altered state of consciousness originating from an altered chemistry in the body is false would be totally unlogical and upright stupid. So if this is what you're saying Burnt, I think you're coming to short on the issue.
With that said I do not claim that everything we experience are applicable to our everyday normal reality and our current knowledge of it, but I am not so narrow that I totally ignore the whole issue and shove it under the carpet just because it ain't part of how we usually perceive things.