That's kind of like saying that a BMW M5 is just a version of a Ford Fiesta. Both will get you there, but the comfort and enjoyment will be somewhat different.
You're right. I'm not that good at metaphors and that one doesn't do the web app justice. My point was that while the two solutions are more or less functionally equivalent, they do differ significantly in ease-of-use and overall comfort.
I'm very, very happy that GitHub is doing this — but I also have high expectations and I do expect the app to improve significantly.
This is huge, because for many people, the current interface to git is the command line, which is too much for people who want GUIs. Yes, there are other GUIs out there, but those are not controlled by GitHub. In this case, they did something very similar to what Google did with Chrome; they wanted to provide a consistent and predictable end-to-end solution for users so they built their own desktop app.
It also does not hurt that the app defaults to use GitHub, though it does seem like you can use remotes that are not GitHub (see repository -> Settings).