Architecturally, it's really no different than a PhoneGap or web app running on Android, iOS or BlackBerry OS. They all involve an "app" typically written with HTML+JavaScript, executed in a web browser (often full-screen and without chrome), which in turn runs on an operating system of some sort.
If it's "native" on Firefox OS, then why isn't it just as "native" on Android, or iOS, or BlackBerry OS, or other mobile OSes?
What I think we really see is Firefox OS totally lacking any sort of real native software development support. This creates the illusion that web apps are somehow "native", when this is just a result of there being no other viable option.