Hi Kansai,
Had a similar problem to yours. I found that by extending both axis ranges to include 0, e.g.,
fig.update_yaxes(rangemode='tozero')
I could align the zeroline of both axes, like so:
Furthermore, constraining the axes to scale with each other causes their values to line up completely:
fig.update_yaxes(rangemode='tozero', scaleanchor='y', scaleratio=1, constraintoward='bottom', secondary_y=True)
fig.update_yaxes(rangemode='tozero', scaleanchor='y2', scaleratio=1, constraintoward='bottom', secondary_y=False)
Hope this helps!