I can't go to the section settings

How does the padding of the addon affect the section?

Yes, I confirm. This is an old problem. I wrote about this in the old forum. It is required to move the mouse very accurately to get to these settings. And it is time consuming and annoying.
Increasing padding does not help in any way to solve this problem.
You can try it yourself by simply creating such a structure and try to get to the settings of the inner section.

Also, the negative margin for the first inner section does not work. It can be done through css only. The reason is this code line.

#sp-page-builder .page-content .sppb-section:first-child {
    margin-top: 0;
}

from

Frontend editor

Live view

I see the solution is to make a login to the settings, via the right mouse button.