It has a very specific definition in this context, and this definition requires that the application be represented in a form that's directly executable on whatever CPU is being used by the computer executing the application.
Anything that doesn't match that very simple criteria is obviously not a "native" app.
Maybe a new term is needed for describing this type of situation involving Firefox OS. I don't know what that would be, but I do know that we shouldn't go ruining an existing technical term.