The initial plot is simply the unprocessed analogue output of the CD player though - it's not a case of oversimplifying things as that's all the information there is. Nothing's simplified at all, that's everything the CD player is putting out The Fourier transform (frequency analysis) plots are basically beside the point until we've established whether or not there's a measurable difference larger than experimental error - if there is a difference the Fourier transforms will help in determining exactly what the difference is, but if all you want to know is whether there's an experimentally significant difference you may as well just compare the raw output. It seems there's some misunderstanding over what exactly is happening in the Fourier plots - it's just a mathematical transformation which can be used to resolve a wave into its harmonic constituents. This is categorically not the same as measuring the frequency response of the CD player or the treated disc - it's a way of processing the raw output data to try to get some idea of how any differences arise.