I don't know about all the duplicate entrys, but as far as redirecting www.mysite to mysite (or vice-versa)- the absolute best discussion I have read covering this is from Tom's blog over at Seablick.com
Interestingly, that particular method of redirect will absolutely introduce a duplicate url (the redirect will land on "mysite.com/default")... I don't know if that has been resolved yet (I am just living with it)
The version of friendly urls that Bruce is working on has a lot of promise...
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