That really depends on the type of the app and the target device. BTW "the web" is native on Firefox OS.
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.
There will never be access to run native binaries on a Firefox OS device. Web APIs are as close to bare metal that it will ever expose.
Seeing that as "totally lacking any sort of real native software development support" misses the whole purpose of the OS, because the web is native on Firefox OS.