Rashi (DH va'Akati Parich) emphasizes that when the Gemara says that a Gezeirah Shavah can teach through a Binyan Av, it really means a Mah Matzinu (and not a Binyan Av).
But I thought that a Binyan Av *is* a Mah Matzinu - they are different names for the same thing! That is what Rashi seems to say in Shabbos 26b DH u'Parat Lecha, and in Bav Kam 63b DH Hekesha. In fact, Rashi in Zevachim 50a DH b'Vinyan Av seems to say that about the very Sugya he is discussing here, and Rabeinu Gershom here clearly says that as well. So what does Rashi mean here?
Rabbi Rabinowitz, Yerushalayim
That is an excellent point, and in fact the Sefer Eizehu Mekoman here (Rav Friedels) asks your question and leaves it unanswered.
The answer seems to lie in the words of the Sefer Kerisus (Rav Shimshon mi'Kinon, in Batei Midos, Sha'ar 3:2). Although most Rishonim understand Binyan Av the way that you do, the Sefer Kerisus has problems with that understanding. He points out that the Beraisa of the 13 Midos (in the beginning of Toras Kohanim) seems to define a Binyan Av as something that is learned from two different concepts through the method of Mah ha'Tzad ha'Shaveh (i.e., even a Binyan mi'Kasuv Echad is learned from a Tzad ha'Shaveh). In addition, he shows that the Gemara never uses the term Binyan Av when learning from a single source.
He therefore asserts that what is learned from a single source is called "Mah Matzinu" (see Yevamos 7b), which is a separate "Midah," not mentioned in the Beraisa of 13 Midos (since it is such an obvious Midah). When something is learned from two verses, then it is called a Binyan Av.
Rashi here holds like the Sefer Kerisus. He is asking why the Gemara calls this a "Gezeirah Shavah that teaches through a Binyan Av." It is a Mah Matzinu, not a Binyan Av! He answers that the words Binyan Av are "Lav Davka," and they indeed refer to a Mah Matzinu in this case. The Gemara used the words Binyan Av only because that is the way that the Gemara mentions this rule in Zevachim 50a.
With the help of Otzar ha'Chochmah, I found that Rav Eliyahu Mordechai Rabinowitz asks your question and gives my answer (without quoting the Kerisus) in his Ner l'Ma'or, end of Teshuvah #65. He also asks from some of the other Rashi's that you mentioned. However, now that we have the Vilna edition of the Shas, it would seem that this is not a contradiction at all. The Perush Rashi here is not the original Rashi. You will notice that for this Perek, a "Rashi Ksav Yad" was printed alongside the Gemara. That is the true Rashi; the other "Rashi" must be a Rishon from the school of Rav Shimshon mi'Kinon, as I mentioned.
Best wishes
Mordecai Kornfeld