Question: Does the sidewiki area indicate in any way that it is not part of the website? Does the url bar only show the sites url, or does it also show some indicator of the side wiki?
It comes with a border, it's blue, it has a title "Google Sidewiki" and it displays your name. I would say it can't be confused with the components of the website itself, although with Web 2.0 sometimes sites get built in a way that components that are parts of the site look like they're not.