Answer

Several later authorities (Acharonim) discuss the fourth principle: that one does not count commandments that encompass the entire Torah. This is what Rabbi Abraham Isaac Kook and Tzitz Eliezer wrote, for example. But this is of course a mistake. The commandments that encompass the entire Torah in the fourth principle are commandments that say, "And you shall keep all My commandments," which are not counted because of redundancy (since there are already commands for each individual commandment, there is no point in counting a command that includes all of them). Regarding settling the Land of Israel, their claim is that it is so very fundamental that it is not counted. That principle appears nowhere in the principles.
As an aside, I’ll say that in my opinion this principle is correct, even though it does not appear in the principles (this is how I explained the commandment of repentance, the issue of free choice, and character refinement). One can discuss why Maimonides did not write it as a separate principle. Perhaps it is because of what he says in the first principle, where he explains that he included only matters that are disputed (even if they seem obvious to him) or matters that are not obvious. Perhaps this principle was obvious to him. This requires further analysis.
But in my opinion, although this principle is indeed correct also within Maimonides’ approach, it is not the correct explanation for the commandment of settling or conquering the Land. There is no indication that Maimonides sees conquering or settling the Land as such a basic foundation in the way Rabbi Kook and his colleagues presented it. In my opinion, this is an invention of Religious Zionist ideology. On the contrary: even Nachmanides, who does indeed view settling the Land this way (for in his commentary on the Torah he explained that all the commandments outside the Land are only in the category of "set up markers for yourselves"), nevertheless counts this commandment specifically (positive commandment 4 in his additions).
In my opinion, it is not counted because according to Maimonides, settling the Land and conquering it are preparatory means for a commandment, not a commandment in themselves. These are conditions for fulfilling the commandments dependent on the Land. And in the tenth principle he writes that one does not count preparatory means for a commandment. If I am right, then this commandment indeed is not counted because of a principle that appears in the principles.