Search engines use the canonical url which by default will be the page url like http://www.xyz.com/home.aspx would be the default for the home page in mojoportal, but if you go to the page settings for your home page and click the Search Engine Optimization tab you will see a place where you can override the canonical url. This was specifically added for the home page scenario you describe, you could enter http://www.xyz.com as the canonical url override there and search engines will treat the canonical url as the correct url for the page in search results.

For all other pages than the home page the default behavior is generally what you want. Really without overriding the canonical url google should be seeing http://www.xyz.com/home.aspx as the canonical url unless you are using some really old version of mojoPortal that was before we implemented canonical urls or unless your url re-wring is somehow interfering with it, but when you view the source of the page you should see the canonical link in the head and search engines should treat that as the definitive url for the page regardless of whether the page also works with other urls.

Hope it helps,

Joe