Daf Yomi - Yoma 56 - Rishonim said אתה כוננת

The Gemora relates that there was one who said over a certain version of the order of the kohen gadolon Yom kippur. the Gemora asks on it and corrects the version. This way is the way it is said in the nusach of אתה כוננת which is nusach sfard. The Ritva says this explicitly that this was the nusach that was said. שערים מצויינים בהלכה quotes Rashi and Tosfos that they also said אתה כוננת which is a bit odd, considering that their main nusach was אשכנז.

The Noda Beyehudah's son (113) brings down different proofs that even though something might have been recited in one of the Tefilos, we cannot bring a proof from there as to what the halacha is. One of the proofs is from our Gemora which stated that the version which was said over in front of Rava was half like the רבנן and half like רבי יהודה. I'm not sure of the proof, because that was precisely the Gemora's קשיא and the Gemora was forced to change due to that, so if anything it is a proof the other way?