The Applesauce is at the mercy of the analog board in the drive. Artifacts of the signal processing done there are going to be reflected in the data stream the Applesauce receives from the drive.

A more authentic representation of the flux on the disk could be made by amplifying and sampling the analog waveform straight off the drive heads. A variety of signal processing functions could be applied to that waveform vs. what the electronics on the drive will do.