Makos, 10a & 13a: Because the two sets of Arei Miklat differ in two ways: 1. Whereas the six initial towns are Kolet (protect a murderer against the Go'el ha'Dam, and forbid him to leave before the Kohen Gadol dies) irrespective of whether he is aware that he entered an Ir Miklat or not, the forty-two additional towns are Kolet only if he knows that it is an Ir Miklat. 2. Whereas a murderer in one of the six initial Arei Miklat is exempt from paying the Levi'im rental for his apartment, in one of the forty-two, he is obligated to pay. ¹

Oznayim la'Torah: Because it is of paramount importance for the Arei Miklat to belong to the Levi'im - either because, as opposed to any of the other tribes, whose inhabitants would be prone to avenge their murdered relatives by killing the Rotze'achat least by treating him wi1th contempt, the Levi'im had particularly refined Midos, and had already proved their ability to control their inner feelings by the Eigel, ¹ and would refrain from doing the Rotze'ch any harm or because, in their capacity as teachers of Torah, they would teach the murderers to do Teshuvah and to follow the right path. ²

Oznayim la'Torah: In connection with the six Arei Miklat, it writes one "Titnun" regarding the Levi'im and one, regarding the murderers - to teach us that the six Arei Miklat are given to the murderers too, which explains why they are not obligated to pay rent, whereas the forty-two, are given to the Levi'im exclusively, in which case, the murderers are required to pay rent - as Chazal have said. ¹

Hadar Zekenim; Da'as Zekenim and Rosh (all in Devarim 15:2, citing Makos 2:8): It implies that, if a murderer is exiled to an Ir Miklat, and the residents want to honor him, he must inform them that he is a murderer; ¹ and only after they insist on honoring him, is he permitted to accept the honor. ²