It uses (by purpose) the same session though as the main Chrome instance.
But it should be possible to implement an option to use a separate session. This might even be much simpler than my current approach (which not only shares the session, it also uses the same Chrome process).
I like the idea, but I'm not sure if I can trust this level of sand-boxing. Does it also use a separate cache (web history, etags, image cache, web cache, etc)? a separate Flash storage? Silverlight storage? HTML5 storage? If any of them are shared, something along the lines of Evercookie would have no problem maintaining cookies across the apps.
Cache is completely separate, Flash and Silverlight (and plugins in general) aren't sandboxed, which is why I deactivated them for my Facebook Browser. (no more embedded youtube videos, but they open in my main browser, works just as well)
Now I have a nice separate window for browsing Facebook and nothing but Facebook.
Separate cookie store is awesome.