In my mind, there isn't much difference technically the big question is whether users want a different experience. A certain percentage want a more fluid user flow similar to a native / desktop app. This web app seems to accomplish that using Google web toolkit and decent page load times.
Right, but since Chrome's app environment is really just the browser's javascript and rendering environment (perhaps with access to a few special javascript apis) there isn't really anything special about #2 either. In fact, apps that fit into your #1 and #2 bins are the same thing modulo caching.
I don't think a XULRunner-like environment has ever been on the Chrome roadmap though. Chrome's been pretty consistent in its intention to expose only v8 + webkit as its extension and app environment, although things like native client are blurring this somewhat.
1) A link to a website, with the link hidden. Going to the actual website provides the exact same experience.
2) A packaged app that is downloaded and contained within the browser. (It may or may not use a web API for some functionality.)
#1 is basically just a bookmark. There's nothing special about it.