As explained in the Container Overview article, typically a website can have two containers viz: Primary Container and Secondary Container.

Primary Container is where the main content appears, whereas Secondary Container consists of the sidebar and various different widgets in the sidebar.

When you select the “Box Layout”; the individual containers and widgets appear in boxes.

You can find the setting under Appearance > Customize > Layout > Container

You can change the background color from Colors & Backgrounds > Base Colors

Other Notes:

You can apply boxed container for selected pages or posts from meta settings.