It's my understanding that part of the possible explanation of mystical visions comes from the work of Wilder Penfield, M.D., a neurosurgeon, who helped create/invent homunculi maps of the human brain. During a brain surgery, he would touch a different part of the human brain with an electrode and the patient who was awake would report what they felt or thought.
It was Penfield's work plus a number of other people including chemists who provided insights into certain drugs which tend to act as hallucinogens plus observations about states of awareness associated with beta, alpha, theta, and delta waves that when put together can explain some mystical visions. Some of these mystical visions or a tendency toward religiosity are associated with TLE (temporal lobe epilepsy) of the right hemisphere (more so than the left hemisphere).
A very loosely related node: Ketamine and Near Death Experience