I don’t see a disagreement between us. The “Karaim” as clearly described by the Gedolim you quoted are a very accurate description of what many call today’s “Modern Orthodox”, laymen that unintentionally misunderstand some fundamentals.
The clear “honesty, innocence, and deep respect for the real Gedolim” that the Rambam describes those mistaken “karoim” is s stark contrast to the last section of the Rambam you quote about kofrim, apikorsim, that aptly describe nearly all sell-proclaimed “Jewish” michallei shabbos bfarhesya today. That Rambam spell is out clearly, which is why I don’t see where we disagree.
If your point in bringing that last section is because of his point about “tinok sh’nishba”, I don’t understand why you omitted the last words of that Rambam that says regarding them “בתשובה ולמשכם בדברי שלום עד שיחזרו לאיתן התורה ולאימהר להרגן”. Being a “tinok sh’nishba” doesn’t change much, with many Gedolai poskim clear that a michalel shabbos b’farhesia specifically can never be considered a tinok sh’nishba, because it specifically is always a clear rejection of Yiddishkeit.
Beyond all there, there is some nuance, as I explicitly said, regarding the psak halacha for many of these practical halachos, like ribis and the like. For example, one contemporary stance in some poskim is that the classic “red line” of shabbos has become so blurred in modern time, R”L, that many Jews thinks breaking shabbos is “perfectly Jewish” because it is so normalized. As such, the psak is to be machmir on both sides.
However, none of this overrides the fundamental need for the Jewish heart to fully hate anyone who hates Hashem.