Well, language is like that. :) But I don't think describing Emacs as "native" here is very different from how the word was used decades ago. To me, "native" is less about how the logic is represented (compiled vs. interpreted code) and more about its execution context. If the host system is an operating system, then the application is native; if the host system is another application, then it's not. I agree that the boundary is blurrier for applications that have scripting interfaces; but I think that most applications don't live very close to that boundary, and are clearly in one camp or the other. (Maybe Emacs is nearer to the edge: there's an old joke that Emacs is a great operating system, it just needs a better text editor.)

Having said all that, I don't think that "non-native" is a pejorative. I use Emacs, but would switch to a "non-native" editor if there were a good reason. I use IDEA (native or not? you decide!) when working on big Java projects, and Emacs for everything else, because Emacs affords me a lot of power that I find lacking in other editors. "Nativity" isn't really part of the equation, it's really about functionality.