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It seems to be working properly irrespective of the presence of null dataPoints. Please take a look at this updated JSFiddle which has dataPoints without null data.
The auto-calculated range of axisY depends on multiple factors which includes y-values of entire dataSeries. In the JSFiddle that you have shared, the minimum and maximum y-values of both the dataSeries are different. Because of the different range of y-values passed in dataSeries, one axis has a negative minimum and the other doesn’t.