Yom Kippur 1 - Machzor Masores HaRav to the Rescue!

The minyan where I davened maariv, mincha, and ne'ilah this past Yom Kippur utilized the newly published Machzor Masores HaRav, with the commentary gleaned from the works of the Rav. Two consecutive comments that I read in the commentary were of special importance to me, one because it answered a question that had bothered me for a long time and one because it resolved a halachic question that I had.

The first issue was regarding the omission of Aleinu from the end of Mussaf. The commentary on the bottom of the Artscroll Zichron Yosef machzor, Aleinu is omitted because Mincha usually follows Mussaf immediately, so that they are considered one long service, and thus should not be separated by Aleinu, which is used to conclude a tefillah. However, why is Aleinu still not said even in minyanim in which there is a break between Mussaf and Mincha (as was the case in the two shuls in which I davened, enabling me to walk the 1.5 miles between them during their concurrent breaks)? The Rav, based on the Rambam in Hilchos Teshuvah (2:4), suggest that even where there are physical breaks in the davening, our tefillos have still not reached completion as long as the day of Yom Kippur continues, and for this reason, we do not say Aleinu. Based on this, though, I don't understand why we would say Aleinu at the end of maariv.

The second issue was a halachic question regarding which trop to use for the leining of mincha, whether it should be the special trop of the Yamim Nora'im or the regular trop. The Rav ties this question to a machlokes between the Mechaber and the Rema over whether one should say the full 4 brachos following the haftara of mincha (Mechaber) or whether the reader should conclude with the bracha of Magen David (Rema), implying that Yom Kippur afternoon has the status of a Ta'anis Tzibbur, rather than the same unique status of the morning and to a teshuva of R' Akiva Eiger in which he says that, while one not fasting is allowed to get an aliyah on Yom Kippur morning, he is unsure if the same applies to the afternoon, due to its possible status as a ta'anis tzibbur. The question of the proper trop to use in the afternoon, concludes the Rav, is also dependent on whether the leining is mi-din Yom Kippur or mi-din Ta'anis Tzibbur. (The Rav notes that the haftarah of Yonah is also thematically a support to the idea that it's a ta'anis tzibbur).