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An instantaneous volume change can result in a click. A linear ramp avoids this
and may prevent speaker damage.
The original experiment probably used a linear or raised-cosine ramp at the start and end of each individual tone (the paper isn't very clear, but raised cosine is pretty standard for hearing experiments). This change doesn't go that far, but it uses a linear ramp any time the gain changes. I find the difference particularly noticeable at the end of each treatment cycle.