My opinion is that you can not use music theory for music composition to create some algorithms that produce music understandable by humans. My view (opinion) is that I should not look at music composition like a programmer; a programmer does a very different job. Like in number theories, you can create patterns with Algorithms, but does it sound great? does an arpeggiator sound great? Sure, but is it composing something? Why are some piano players great and some not so great if they are playing the same notes? Music works on so many layers that until now, no music instrument builder has developed a Turing machine-like approach like they have in computer science.
I think Algorithm composing is the wrong tool for this job.
- Experimental music
You do not want to make music that's based on something that's not new or known to us
and an Algorithm could only work with known solutions (Determinism problem).
You cannot prove some thing in music; music has no right or wrong state. What is the right state in music? How can an Algorithm prove that it has produced a good music piece when the problem is deeper. Music is an experience thing without meaning; it is like feeling something. Until now, we do not have some thing like AI. All we got are some pattern recognition algorithms that can see patterns; you can't make music without Consciousness.
- Historical music (pop music pattern , rock, techno , baroque, etc.)
There are known pattern for this music. Music theory is not something that is creating those patterns; music theory is more an analytical approach.
Maybe I can recommend you the book of Roger Penrose, "The Emperor's New Mind"
Penrose presents the argument that human consciousness is non-algorithmic, and thus is not capable of being modeled by a conventional Turing machine-type of digital computer.
I think consciousness is a Precondition to create human understandable music or you can not produce Culture without the human factor.
Well, I'm not sure if you can get my point.
To shorten it up:
Music theory is more an analytical approach, but you have to have some data to analyse
(limits of music theory -> lack of Creativity)
Know the limits of an Algorithm (like http://en.wikipedia.org/wiki/Entscheidungsproblem)
If you know these limits, you can get good tools to produce.