I'm facing the same problem as the user reported in https://stackoverflow.com/questions/63523328/plotly-secondary-y-axis-causes-empty-space-on-the-right. I'm using the latest version of plotly and it doesn't seem to be resolved since 4 years ago.

For some reason, when adding secondary y-axis, the margin calculation seems to ignore the second y-axis, despite setting margin in the update_layout.