What does the din of "makom goreim" with respect to dinei nefashos have to do with kiddush hachodesh? Apparently the Ramban understood that "makom goreim" is a halacha in beis din, not in the particular process of dinei nefashos. When beis din is not located near the lishkas hagazis, they lack their full status and authority. Therefore, kiddush hachodesh, which was done even after the sanhedrin was forced to move, must not require the full authority of beis din hagadol to be carried out.
R' Zolti in his Mishnas Ya'avetz asks: If this is correct, why then according to Ramban is there a chiyuv to obey and not rebel against the sanhedrin even when they were sitting in Yavneh (as the Sifri darshens)? How could there be a chiyuv of "lo tasur... asher yagidu lecha min hamakom ha'hu" if beis din lacks full status/authority when not in lishkas hagzais?
He answers that Ramban follows the view of the Chinuch that lo tasur prohibits not just rebelling against beis din hagadol, but rebelling against any of the gedolei and chachamei hador of any time. Rambam l'shitaso that there is no diminuation of the chalos shem or status of beis din even if they are not sitting near lishkas hagazis disagrees and learns that lo tasur applies only to the sanhedrin, but not to every beis din or chacham.
It's interesting to compare the approach of R' Zolti, who was a Brisker, with that of another Brisker -- R' Soloveitchik (see Koveitz Ch. Torah). RYBS suggested that there are two roles of sanhedrin: 1) the supreme court; 2) the bearers of the mesorah of klal yisrael as their representatives. Kiddush hachodesh according to the Rambam is not a function of B"D's role as supreme judicial body, which, as Ramban correctly notes, came to a close long before the churban. Rather, it is a function of their role as bearers of the mesorah in their representative capacity. Based on this, there is no reason to align the Rambam against the Chinuch l'shitaso. When the Rambam mentions beis din hagadol in the context of lo tasur, he might be referring to beis din as transmitters of the mesorah of klal yisrael, a role that is fulfilled by the chachamim of each generation.