Hello,
Custom positions do not show on the Main / Layout page, that page is just for core positions.
Custom_3 is not the same as the below_body positions, but they are very similar, those positions would display under custom_2, while custom_3 shows next to custom_2 and never under it. Custom_3 shows strictly under the component area and is contained by the columns around it.
You can review the layout here:
http://www.shape5.com/demo/game_world/index.php/features-mainmenu-47/template-features/module-positions