The override for the TopIdentifierList parameter doesn't work if the the file menu.ini.append.php is located in any extension or siteaccess settings folder.
Example:

<?php /*

[MenuContentSettings]
TopIdentifierList[]=article_mainpage

*/ ?>

Steps to reproduce

Just copy the code above in menu.ini.append.php and save it in any extension or siteaccess settings folder and create an Article (mainpage) object under root. It doesn't appear in top menu.