Meditation as understood by the Buddha is based upon an ontological foundation that goes much deeper than what classically oriented natural science has been able to provide. To be sure, the depth of the human mind goes beyond the brain.
The mind-brain connection is a very real connection except that the mind cannot be described in physical or biological terms. No amount of forcing mind to be subservient to the brain, or just ignoring it, will work anymore. It is like trying to get people to believe that music comes from the single radio sitting on the book shelf. Such a view ignores the ubiquitous radio signal. Likewise, those who postulate that the human brain is primary ignore mind.
The real goal of meditation is to penetrate through the psychophysical body, even going beyond its space and time position, all of which amounts, simply, to a return-to-self (absolute verification). But this is also not only a return, but also seeing, for the first time, that mind is all-penetrating. Nothing stands in its way insofar as all things are its configurations. This is mind as absolute.
Hitherto, the adept was bound down to phenomena, even the adepts own subjective world. The adept's mind was in a state of dependence; attached to the psychophysical organism. The adept lacked the right vision/insight to get beyond the configurations of mind including both the outer and inner world.
Buddhist meditation really has nothing to do with physical positions such as sitting. It has everything to do with complete transcendence; or realizing that we are free, immaterial spiritual bodhi-beings. Nothing can bind us because everything is of a spiritual substance which is what we are. Things are our projections.