Thank you for the report. We want to make the transition to PyFerret as simple as possible with few script changes. I'll look into the right_axis_plot.jnl script. I would expect it to work correctly in PyFerret. Your example figure looks to me as if some aspect of the scale and location information is being lost.
One possible workaround for this kind of plot is to use multiple identical viewports, drawing only the desired plot axes in each one. Here is the idea; one would need to do more to add the correct labels