The site map treeview can be styled by css like anything else. We use the CSSControl Adapters to make it render as a more semantically correct set of ul li elements instead of the nasty nested tables that the normal asp.net treeview uses.
I don't recommend changing mojoPortal code or you will have problems upgrading without losing your changes.
You can use extensionless urls, it does not depend on routing.
http://www.mojoportal.com/extensionless-urls.aspx
Hope it helps,
Joe