Parshas Shemos:Shem HaMeforesh

HKBH tells Moshe "Zeh shimi l'olam v'zeh zichri l'dor dor". The gemara in Kiddushin learns from here that one must pronounce the shem havayah with the shem adnus. The Brisker Rav and Rav Moshe both have the following chakirah:

When one says the shem adnus are you really reading the shem havayah or are you reading a different name of HKBH.
This chakirah can also be asked by a regular kri u'kisiv. However, both the Griz and Rav Moshe point out that the halacha by the shem hameforash is not the same as a kri u'kisiv. It is a different halacha which applies anytime you say Hashem's name.
Both Rav Moshe and the Griz hold that you are really reading the shem havayah. However, by a regular kri u'ksiv they disagree. Rav Moshe holds you are reading the word that is written while the Griz (Griz al HaTorah Parshas Va'Eschanan) holds you are reading a different word.

Nafka Mina

1) If part of the shem hameforash is covered with wax do you need to take out another sefer torah. Rav Moshe writes that if you assume the shem adnus is a different name than the shem havayah so you can argue that you were never reading the shem from the klaf. It was always ba'al peh. Therefore, even if the word is covered by wax you can still read it. However, since we hold that by reading the shem adnus you are really reading the shem havayah, so you must get another sefer torah. (According to this l'fi the Griz by a regular kri u'ksiv you would not need another sefer torah)

2) The Rambam in Hil Avodah Zara 2:7 has 2 opinions if you are chayav misa for being m'kaleil with the shem adnus. The Brisker Rav (al HaRambam AZ 2:7) writes that it is toloi on the chakirah. If by saying the shem adnus you are really saying the shem havayah then you are chayav misa, but if it is a different name than you woul dnot be chayav.

3) The Mechabeir and GRA in Orach Chaim Siman 5 argue what kavanah you need to have when saying shem Hashem in davening/berachos. The Mechabeir holds you need kavanah for shem havayah and shem adnus. The GRA holds that you only need kavanah for shem adnus (except for Shema where you need both). Achronim explain the machlokes is based on the chakirah. The Mechabeir holds shem adnus is same as shem havayah so you need kavanah for both. The GRA holds the shem adnus us a separate name and all you need kavanah for is shem adnus.