mw13: To answer your question without getting too political, there are two basic differences.
The first is that people meeting with people like Ahmedinejad and supporting the worst of anti-Semites is, without exaggeration, endangering Jewish lives.
The second (and much more important) is that no one would ever view the unaffiliated or completely secular Jew as legitimate. No one thinks that they are doing something acceptable in Judaism. It is precisely because the Niturei Karta are Makpid on things like Shabbos, Kashrus, and more that there is this danger. People feel the need to separate themselves from the close but illegitimate neighbors. If you talk to them about things other than Zionism and supporting Anti-Semites, the Niturei Karta would be indistinguishable from this Chareidi author. Therefore, the Chareidi feels the need to show, in no uncertain terms, that this person’s path in Judaism is entirely illegitimate. (It is very, very similar to the YU/Centrist community’s reaction to Open Orthodoxy, which is also much stronger than their attitudes towards other not-Frum people.)