Tosfos (R”H 17) quotes a machlokes Rishonim as to what the 13 midos are. According to R”T, Hashem Hashem counts as two midos: there is Hashem’s rachmanus before the cheit, even though he knows the person will fail, and then there is rachmanus after the cheit. R’ Nisim Gaon disagrees. He reads the pasuk that introduces the midos as follows: “Va’ya’avor Hashem al panav vayikra Hashem,” Hashem called out and recited 13 midos, “Hashem K-l erech apayim…” etc. In other words, the first Hashem is connected to “vayikra…,” not to the list of midos. To get to 13 he counts notzer chessed as a separate midah from l’alafim.
The Rosh brings proof that R"T right form the nusach we all use when we say slichos. Have you ever heard a shat”z say, “Va’ya’avor Hashem al panav Vayikra Hashem,” and then pause? Neither have I. It’s always, “Va’ayavor Hashem al panav vayikra,” pause, then the midos, “Hashem Hashem…” Awhile back when I discussed this with my son I told him that given that we say the 13 midos so many times, especially in the slichos of erev Rosh haShana, it would be clever of a shat”z who knows this machlokes to read the pasuk like R’ Nisim Gaon and put the pause in a different place maybe once in order to be yotzei his shita. After thinking about it again this year I don’t know if that would be right. R’ Nisim Gaon probably knew the nusach we use too -- maybe it was even the nusach in his shul -- but maybe he didn’t care. Who says nusach can serve as a proof? Rav Wahrman here collects a bunch of examples where the text of a bracha is used as evidence as to the nature of a mitzvah or a halacha, e.g. (since it's the season) whether the bracha is lishmoa/litko’a/or al tekias may indicate to whether the mitzvah of shofar is listening or blowing. Here though, it’s not the text which is in question –- it’s the same words whether R”T or R’ Nisim Gaon is right -- but it’s the nusach hatefilah, how you punctuate the sentence, which changes.
Whatever R”N Gaon held, you see that the Rosh took the nusach seriously enough to pasken from it. The Rosh thought the nusach should accurately capture and reflect the meaning of the words. Sometimes a well meaning chazzan tries to stick a nice tune into the tefilah to get people involved and singing, but the meter doesn’t quite fit -- a word from phrase A gets tacked to phrase B, or a word gets dropped that should be there, etc. When you chop up phrases the wrong way, the nusach obscures the meaning. It’s nice to sing, but it’s also nice for the words to make sense.
The Rama writes that we don’t tamper with the nusach hatefilah of R”H and Y”K – it is as much part of the mesorah as the words are. Way back when I was in YU I remember Chazan Beer giving a seminar to the smicha students and bringing out this point with a story about the Chofetz Chaim. The C”C was called up for an Aliya on R”H or Y”K and paused for a long time before he finally said the brachos. When asked about the pause, he explained that he could not remember the tune, the nusach, and had to give himself a minute until it came to mind. He didn’t want to just say the brachos like it was an ordinary Shabbos – he wanted to make sure to use the right nusach.