As you point out, the distinction isn't necessary for many novices. Yet Apple is making the distinction a fundamental aspect of their gesture model.
Sure, web apps are getting closer to native apps and that's a great point (why is switching between web apps that much different than switching between spaces). However, most web pages still tend to look much like a web page and I maintain that people will discover the concept of different applications by associating them with what comes up once they click the dock icons (iCal, Mail, Settings).
Another point is that if this distinction is useless to novices (e.g. they don't use the gestures or they don't "get it"), then the more experienced users can pick up on this, and take advantage of this knowledge. Just because it's a fundamental aspect of the gestures does not hurt the novice aspect.
Your contrast of versions of Windows and Office is an apples and oranges comparison. People don't know that difference because it doesn't matter and there is no reason to even discover that difference.