Rabbi Isaac of Komarna has a different explanation of why the Rambam doesn't count settling Eretz Yisroel as a mitzvah. He contends that the Rambam basically agrees to the Ramban that there is a mitzvah to conquer Eretz Yisroel and that we must not leave it in the hands of gentiles or unoccupied. However, he holds that it cannot be counted among the 613 mitzvos because we do not count mitzvos that are not within human power to fulfill. For example, prophecy is central to Judaism, yet there is no mitzvah for a Jew to be a prophet, because a Jew cannot select that status for himself; it is up to G-d to give it to him.
Here too, the conquest of Eretz Yisroel, no matter at what point in history, was not something that the Jews could just do on their own. They needed to be commanded by a prophet to do so. The conquests of Yehoshua and David, as well as the establishment of the Second Commonwealth in the time of Ezra and the Men of the Great Assembly, were all accompanied by commands from the prophets of the time. But in the absence of a command, Jews are forbidden under oath to rebel against the nations, and we must accept exile with love until the coming of moshiach. When moshiach arrives, the restoration of the Jews to Eretz Yisroel will not take place naturally, but through prophecy and wonders. Thus it cannot be counted as one of the 613 mitzvos, for the mitzvos were given to men of flesh and blood, not to prophets who change the laws of nature. (Otzar Hachaim, Kitzur Taryag Mitzvos, p. 59)