update_yaxes behavior for make_subplots vs specifying axes directly

--copied from the plotly forum here https://community.plotly.com/t/update-yaxes-behavior-when-using-make-subplots-vs-specifying-axes-directly/92496--

To my knowledge, there’s two main ways to create subplots:

make_subplots(), then add trace data - example here
create list of data, inject into go.Figure() - example here (see hover on subplots)

I’m not sure which one’s the preferred one, but update_yaxes affects them differently.

If we use method 1, the update_yaxes affects all yaxes as intended
If we use method 2, the update_yaxes only affects the first subplot

Is there a reason why update_yaxes doesn’t play well with the second way of creating subplots?

Start with the two linked examples in the issue and reproduce the differing update_yaxes behavior using make_subplots() and a manually assembled go.Figure(). Trace how subplot axes are referenced in each case. Done means the discrepancy is resolved or its intended behavior is clearly documented with a regression example.