I know this is an old post but just in case you still want to know:

'Creates a secondary index on the identifying columns on the change tracking side table at enable time'. This allows creation of a secondary index for changetracking tables, which we heavily use for replication between Configuration Manager sites.

http://blogs.technet.com/b/smartinez/archive/2013/03/06/sql-for-configmgr-2012.aspx