Hello,
It looks like the plugin adds its custom functionality on checkout page using the standard WooCommerce hook. When you create a custom layout with Elementor it doesn’t contain any default elements and hooks. It contains only those elements that you added with Elementor manually.
We have a special “Hook” element in Elementor that you can place to your custom layout and then the plugin will be able to add its custom content there. But we don’t know which one exactly it needs. You can either try to select all hooks one by one or contact plugin developers for help.
Kind Regards
XTemos Studio