There is no way to align multiple axes except by setting the viewWindow for each. But if you only want to align the 0 values, and all data values are positive (for example), then it should be enough to set viewWindow.min to 0 for both.
Given dynamic data, and if the above simplification doesn't apply, then you could do the necessary computation to determine where the min and max need to be for each axis such that the 0 values align. Not trivial, but possible.
This is something we should try to add as a standard feature since many people request it.