Created from #2053 new addition from Otto42:
The pluggable.php contains this code in wp_notify_postauthor():
$wp_email = 'wordpress@' . preg_replace('#^www\.#', '', strtolower($_SERVER['SERVER_NAME']));
This is done because it builds its own headers and sends them to wp_mail. The end result of this is that the wp_mail_from filter is not applied in this case, because $headers != .
Suggest changing the code above in wp_notify_postauthor() to this:
$wp_email = apply_filters('wp_mail_from', "wordpress@" . preg_replace('#^www\.#', '', strtolower($_SERVER['SERVER_NAME'])));
In order to apply the same wp_mail_from filter to these email addresses as well.