Fourier series uses a convergent approximation to plot a harmonic. You can only compare fourier series when A and B are of the same signal type, Periodic, Semi, ect. Music is a combination of harmonic signal types and turns out can not be compared with a fourier transform.
This article basically sums it up: Music signals can not be accurately compared. Convergence is a bitch.
I'm a little confused by your statement, but I think you are confusing Fourier Series with the Discrete Time Fourier Transform. They are not the same thing. What do you mean by "Convergence is a bitch," and where in that wikipedia article does it say that "music signals can not be accurately compared"?
Edited by ultrabike - 7/26/12 at 2:53pm