How can I use default CPT templates from sub-folder?

I think you should use single_template filter hook to load your template from a subdirectory. The full code will be like below-

function the_dramatist_get_custom_post_type_template($single_template) {
    global $post;

    if ($post->post_type == 'your_post_type') {
        // Your post type directory with the post type template file name
        $single_template = dirname( __FILE__ ) . '/post-type-template.php';
    }
    return $single_template;
}
add_filter( 'single_template', 'the_dramatist_get_custom_post_type_template' );

Please read the documentation for further information. Hope that helps.