I recently attended an academic workshop on algorithmic music in Common Lisp and wrote some relevant code in Clojure while there. A lot of people there had strong music theory backgrounds and were very interested in both alternate tunings and the "set theory" approach to pitch sets.

The good news is that with Overtone (the Clojure interface to SuperCollider) you can specify individual pitches rather than MIDI note numbers. People at this workshop who wanted to work with pitch sets or unusual tunings had to resort to controlling the pitch bend programmatically, which, while it certainly works, involves a lot more effort and results in less elegant code.