Setting a Canonical URL domain at admin -> SEF URLs will also set the default website url that will be used for mail template and other places (not download link). If you have a tiki installed in one domain (as well several sub-domains that redirect to this domain) but want your link to display another domain you own you can do this by setting the field with it (like the Wordpress website url setting).
IE: your Tiki is published at "http://tiki.mycompany.server1.com" and you want mail templates (mail validation) and the tiki to use widely and be referenced as "http://www.mycompany.com".
Important : it will also set the url being used for FaceBook and Twitter.