As shown here it seems as if panels can be divided vertically to combine them in one column.
How can I resize or split a panel to achieve that?
I am using Windows desktop version. Currently, I have only vertical panels and positioning options are only horizontally left/right. Up/down arrows are disabled.
Also if you have already found the "Change Application Layout" option it seems that the options to move panes is reasonably limited using "plain" Joplin. You can change the horizontal order of the panes and you can combine the Side Bar and Note List using the left arrow on the Note List (or the right arrow on the Side Bar). "Change Application Layout" becomes more useful as you add plugins that add panes to display their data.
I only use the tabs plugin. With that one it appeared on the far right. I was able to use its left key to combine it with the pane to its left and then the up arrow to push it to the top.