Assuming that $GLOBALS['Pootle_Page_Builder_Render_Layout'] carries an instance of Pootle_Page_Builder_Render_Layout, the method panels_render() returns a string.
So you can simply pass the method call as an argument to apply_filters():
$content = apply_filters( 'the_content', $GLOBALS['Pootle_Page_Builder_Render_Layout']->panels_render( $page_data->ID ) );
I’m not sure whether this is an intended use of the API of the plugin, as Pootle_Page_Builder_Render_Layout::panels_render() remove some default filters from the content (wptexturize, wpautop and convert_chars). So maybe your concern is also worth a question on the plugin support forum.