The best solution to the SEO issue is to override the canonical url on your home page. For example on this site the Home page is a page named "Home" and while it will also return the home page using the url /Default.aspx, mojoPortal by default uses the specific page url for the canonical url, so in my case it made the canonical url http://www.mojoportal.com/home.aspx. However, for SEO purposes I prefer my home page have a canonical url http://www.mojoportal.com/, so I specified this as the cannonical url override in Page Settings on the SEO tab. For pages other than the home page the page specific url is generally what you want for the cannonical, so this override setting was really added to solve the home page canonical issue.
By specifying the canonical url in the meta it doesn't matter if the link in SiteTitle has Default.aspx in it or not, google will treat the canonical url as the correct url.
Hope it helps,