Multiple magnitudes give a VIRTUAL set of axis for EACH signal displayed. Each waveform, in auto mode, will scale individually as if there is an individual axis for each waveform. This is so that a small signal may be viewed along with large signals. A shift click on each waveform in this mode, the axis labels will change to reflect the scale of that particular signal. The cursor readout however is always correct for each signal, independent of what particular axis is actually displayed. This avoids the increased area that drawing many Y-axis, would otherwise occur. The gain and scale options of the individual waveforms may also be used to achieve the same effect, but this requires more steps.
If the waveform axis and labels appear not correct, make sure to shift click on the required magnitude and phase waveforms to reset the graph. To save redrawing, not all of the graph area is always updated.
The waveform scaling/label code is not very finely polished, and is not fully error correcting. Manual mode settings are not taken literally, they are quantised first. Resizing the graph to another size can clear up out some issues.