Click the button to open the dialog box also accessed from Plot->Plot Type Settings->General Frequency Domain….
When the dialog is opened, note that the settings that do not apply to the waterfall plot type are disabled.
If complex division using the reference measurement is selected in Plot->Plot Type Settings->General Frequency Domain…, the resulting complex frequency response is inverse Fourier thus performing deconvolution. The deconvolved measurement is used for the waterfall computation. The window limits for the deconvolution are set by the window settings. But if Cumulative Spectral Decay is chosen as mode, the Time Window upper limit for the active measurement is set as the end of the measurement.