The web is not going to "win" because the average consumer has been trained to look for "apps" from the app store, not to use web apps. Web apps packaged in the app store might be a bigger thing moving forward, but the point remains - on a phone people expect an app. No amount of needing out over how things "should" be is going to change the basic behavior of millions of users. Instead of hoping the web will win, smart devs will accept reality and make the best of it.
You might reasonably argue that Firefox OS will not get much traction, but denying it's existence as you're doing is foolish, because it obviously exists.
There is no difference between apps and webpages. None. Zero. That's the point of the original article as well: that most apps are just worse implementations of perfectly working webpages.
I agree there's no point in getting a Firefox OS phone if you have a phone with a decently modern browser. Their pricing and hardware positioning appear to be squarely aimed at those places where those are not available.
However, that takes nothing away from, and even supports the assertion, that webapps (or generally, pages that behave like apps) seem more future-proof. They'll work on your "phones with decently modern browser" too, regardless of what happens with Firefox OS.