New experimantal implementation for Highcharts 4.1 is available at http://jsfiddle.net/gh/get/jquery/1.7.2/highslide-software/highcharts.com/tree/master/samples/highcharts/studies/alignthresholds/.
This implementation looks a the threshold on the primary axis (the one first defined), and aligns the threshold of any following axis to that of the primary axis.
@Lukasz, if you start zooming in the 2015 where there is huge difference, the 0 alignment is lost:
if you start zooming, the 0 alignment is lost:
your implementation works fine. Just encounter some issues once user can zoom on the chart. It Any idea on how to force to always display the "0" in the chart?