This has been designed to specifically ensure that duplicate indexes never occur if you actually look at the script.  I have run this script for years with very good results that have never hurt performance.  Our web production database has it scheduled to run every day to ensure maximum performance at all times.  I have yet to see any negative impacts from running this script.  For large database in excess of 50gb I recommend restricting it to top 50 indexes found to avoid creating too many indexes.  I would challenge you to show a weakness in the script as I have yet to find one.  I recommend running this adhoc in large databases as needed rather than scheduling it.  It is not intended to fine tune a database but only to address major indexing problems with minimum hands-on work as necessary.  Fine tuning a database is still a manual process.