Add custom shortcodes to the Welcome Mail

Based on your updated question and comments, this should be what you are looking for:

function wpse_225078_wpbd_tags( $tags ) {
    $tags['one_time_link'] = one_time_link();

    return $tags;
}

add_filter( 'wpbe_tags', 'wpse_225078_wpbd_tags' );

The idea is to hook into the tag system provided by WPBE so you can just use %one_time_link% in your email template.

Please note that this assumes one_time_link is a function in your theme/loaded within the WordPress environment.

There’s no guarantee this will work, but I hope it puts you on the right path.