Okay, there's not a warning in the file marked INSTALL... but a quick look at the index.htm that is contained in the folder says "You will prabably want to replace this file with your own website" before redirecting your browser to their homepage. Why they have you copy the contents of the public_html folder into your own public_html folder is a bit of a mystery to me, since all that you need is the lists folder. I recommend copying only that folder onto your server. I think the index.htm file is there simply to show you where everything goes in relation to your own pages.
In answer to starapple's question, I suppose this could be dangerous, overwriting your index file, if you do all of your editing on-line and don't keep a local copy of your pages. I find this to be a dangerous way to work anyway, especially if you're installing 3rd party software and don't have enough knowledge of how a site works to avoid copying over your only copy of your index file. A better thing to do than asking why the folks at Tincan (who gave you some great software for free) did what they did with your index file is to be careful, read everything before copying over your own stuff, answer "no" or "cancel" when you get a dialog asking if you want to replace your index with the new one you haven't even read yet, etc.
Just my 2 cents