Interest in the spiritual elements of music and sound have been around for hundreds if not thousands of years. Apparently in one Chinese dynasty the court ordered a standardized tuning. A short and interesting article on the history of tuning in western music is at http://www.schillerinstitute.org/music/ ... _hist.html
There are actually two issues involved - mapping a note to a specific frequency and then constructing scale from that note. It seems the Perfect Circle folks are just resetting the frequency for A. The instrument would still play a equal tempered 12 note scale and there are many people who take exception to that.
There is no universal reason to divide an octave into 12 parts unless it is part of the instrument design i.e. a keyboard. The American composer Harry Partch built his own instruments to transcend the limits of 12 equally spaced semi-tone scale. There are many other scales in use around the world.
Music has also been closely tied to colour and example of a composer is at http://en.wikipedia.org/wiki/Alexander_Scriabin
Parallel to this topic is the idea that certain keys have specific emotional resonances.
The suggestion of the Perfect Circle folks that they have discovered secret to higher mystical states seems suspect. Not that I reject the idea of higher states of consciousness or enlightenment. I suppose in the pursuit of enlightenment retuning you instrument is a lot healthier than taking drugs.