Thomas,

I am on GoDaddy's Website Builder as well and had the exact same issue that brought me to this thread.  I did what they suggested and it got rid of my crawler seeing a duplicate with the home.html page.

Here is what I did:

1. In ALL menu navigations, I replaced the links to home.html with the root URL of my domain (like http://myurl.com)  I had to do this for my main navigation at the top of my website and then a footer navigation that I had.
2. Then, for my logo image in my header, I had to change the link from the home.html page to the same root URL.

After I did this, I did a recrawl and now home.html is not being found and therefore, not showing up as a duplicate.

Would have been nice to have been able to put in a canonical reference but you get what you get and for the flexibility of Website Builder for a quick website, I'll take the extra work to get it just right

Good luck!

-Rhonda