It proposes that what we experience as consciousness is built up in a hierarchical process, with various parts of the brain doing further processing on the flow of information and contributing their own part to the "feel" of consciousness. It's possible to subtract various parts of the process, thereby leading to an altered state of consciousness, without consciousness itself disappearing.
The prefrontal cortex is usually associated with "higher-level" tasks, including emotional regulation, but the authors suggest that this is due to the prefrontal cortex refining the outputs of the earlier processing stages, rather than inhibiting them:
"In such a view, the prefrontal cortex does not represent a supervisory or control system. Rather, it actively implements higher cognitive functions. It is further suggested that the prefrontal cortex does not act as an inhibitory agent of older, more primitive brain structures. The prefrontal cortex restrains output from older structures not by suppressing their computational product directly but by elaborating on it to produce more sophisticated output. If the prefrontal cortex is lost, the person simply functions on the next highest layer that remains.The structures implementing these next highest layers are not disinhibited by the loss of the prefrontal cortex. Rather, their processing is unaffected except that no more sophistication is added to their processing before a motor output occurs."
Their theory is that several altered states of consciousness involve a reduction in the activity of the prefrontal cortex:
"It is proposed in this article that altered states of consciousness are due to transient prefrontal deregulation. Six conscious states that are considered putative altered states (dreaming, the runner's high, meditation, hypnosis, daydreaming, and various drug-induced states) are briefly examined. These altered states share characteristics whose proper function are regulated by the prefrontal cortex such as time distortions, disinhibition from social constraints, or a change in focused attention. It is further proposed that the phenomenological uniqueness of each state is the result of the differential viability of various [dorsolateral] circuits. To give one example, the sense of self is reported to be lost to a higher degree in meditation than in hypnosis; whereas, the opposite is often reported for cognitive flexibility and willed action, which are absent to a higher degree in hypnosis.The neutralization of specific prefrontal contributions to consciousness has been aptly called ‘‘phenomenological subtraction’’ by Allan Hobson (2001).The individual in such an altered state operates on what top layers remain. In altered states that cause severe prefrontal hypofunction, such as non-lucid dreaming or various drug states, the resulting phenomenological awareness is extraordinarily bizarre. In less dramatic altered states, such as long-distance running, the change is more subtle."
And about meditation in particular, they hypothesize that it involves a general lowered prefrontal activity, with the exception of increased activation in the prefrontal attentional network:
"It is evident that more research is needed to resolve the conflicting EEG and neuroimaging data. Reinterpreting and integrating the limited data from existing studies, it is proposed that meditation results in transient hypofrontality with the notable exception of the attentional network in the prefrontal cortex. The resulting conscious state is one of full alertness and a heightened sense of awareness, but without content. Since attention appears to be a rather global prefrontal function (e.g., Cabeza & Nyberg, 2000), PET, SPECT, and fMRI scans showed an overall increase in DL activity during the practice of meditation. However, the attentional network is likely to overlap spatially with modules subserving other prefrontal functions and an increase as measured by fMRI does not inevitably signify the activation of all of the region's modules. Humans appear to have a great deal of control over what they attend to (Atkinson & Shiffrin, 1968), and in meditation, attentional resources are used to actively amplify a particular event such as a mantra until it becomes the exclusive content in the working memory buffer. This intentional, concentrated effort selectively disengages all other cognitive capacities of the prefrontal cortex, accounting for the a-activity. Phenomenologically, meditators report a state that is consistent with decreased frontal function such as a sense of timelessness, denial of self, little if any self-reflection and analysis, little emotional content, little abstract thinking, no planning, and a sensation of unity. The highly focused attention is the most distinguishing feature of the meditative state, while other altered states of consciousness tend to be more characterized by aimless drifting."
They do not discuss permanent changes caused by meditation in the paper, but if the prefrontal cortex is involved with last-stage processing of incoming sensory data, then prefrontal regulation would fit together with meditators' reports of being able to experience sensory information in a more "raw", unprocessed form. Likewise, if the prefrontal cortex unifies and integrates information from earlier processing stages, then meditation revealing the unity of self to be an illusion would be consistent would reduced prefrontal activity.
Vipassana jhanas, or other forms of meditation aimed towards reaching enlightenment, would then somehow involve permanently reducing or at least changing the nature of prefrontal processing. Meditation practicioners speak of "the Dark Night", an intermediate stage during the search for enlightenment, which is experienced as strongly unpleasant and where "our dark stuff tends to come bubbling up to the surface with a volume and intensity that we may never have known before". This is achieved after making sufficient progress in meditation, and will continue until the practicioner makes enough progress to make it go away.
Under the model suggested by the paper, the Dark Night would then be an intermediate stage where the activity of the prefrontal cortex had been reduced/changed to such an extent that it was no longer capable of moderating the output of the various earlier emotional systems. Resolving the Dark Night would involve somehow finding a new balance where the outputs of any systems involved with negative emotions could be better handled again, but I have no idea of how that happens.