Hi,
I don't really think there is much difference (but maybe a little) from an SEO point of view since the canonical url is going to be whatever it is no matter how the inbound links are formatted but I think it makes for a prettier, shorter and more natural url to be shown in search results for your home page. Note that if you do specify the canonical override it needs to be a full url with the http:// like http://www.yoursite.com/
Best,
Joe