For instance if I can monitor alpha, beta, gamma, theta wave activity I should be able to probe which practices tend to lead to which states.  If the software can be reconfigured to give alert noises when say beta activity picks up it could act as an early warning that the mental state is becoming agitated before one is thrust out of deeper state...   

This really is more for self interest.  Having read quite a few papers of advanced stage monks being monitored and them showing highly unusual EEG patterns I think it could in practice help lead a person to deeper meditation states faster...  Beyond that I don't honestly know.  I'd need to play with it to see if I could formulate some sound hypothesis to test.