From what I know about these kind of programs is that most of the programming is based on Markov Chains based on the composers previous works.
A Markov Chain is a system where probabilities are assigned to different states, so say using a crude example based on Palestrina:
First Note C:
Second Note: D = 30%, B = 30%, E = 20%, A = 20%
And so forth, so you have a 12x12 matrix with different probabilities assigned to each entry, and then the piece is 'calculated' as a chain moving from one note to the next.
It's something I would like to get into. Personally, I think the idea of trying to recreate a Bach-style piece is intriguing and interesting from a mechanical point of view, but kind of useless from an artistic perspective. However, I think that the idea of Markov Chains and Stochastic Systems can be used to create diffreent ideas. I know Xenakis began to look into that, but as I said, its only something I'm just looking into...