As the gemara goes through the 5 opinions about when bal te'acher is triggered it stops to ask why someone who held one way didn't hold according to another answer. When it goes through R. Eliezer ben Yaakov's answer (2 mo'adim must pass). The other voices are defended by saying that htye hold like R. Yonah who, on Shevuos 10a uses this posuk for equating a mo'ed's chatas and Rosh Chodesh's chatas. But the gemara doesn't ask how R. Eliezer comes to that understanding of the chatas on a mo'ed if he doesn't hold like R. Yonah. Sure, we could say that he holds like another opinion, but the gemara doesn't even ask, let alone tell us which other opinion he holds like. Why?
Dan, Teaneck, NJ
1. The Yefeh Einayim (printed in the back of the Gemara) cites the Toras Kohanim in Parshas Emor (printed in the Malbim Chumash) on Vayikra 23:38 which derives from the word "b'Mo'adeichem" that one does not transgress Bal Te'acher until all of the Regalim of the entire year pass by.
2. This suggests that even though Rebbi Eliezer ben Yakov learns from "b'Mo'adeichem" that two Regalim suffice, nevertheless there is an opinion that does not learn that the least possible number of Moadim is two but, on the contrary, learns that "b'Mo'adeichem" suggests that all of the Moadim must pass by in order for one to transgress Bal Te'acher.
3. According to this, we can understand that when the Rabanan say that "b'Mo'adeichem" comes to compare all of the Moadim, this automatically implies that more than two Moadim are included, and therefore one knows that "b'Mo'adeichem" does not teach us the Din of Rebbi Eliezer ben Yakov, so it is therefore possible to derive a different Din from this verse -- namely the Hekesh of Rebbi Yonah.
4. So when the Gemara states that b'Moadeichem teaches the Din of R. Yonah this automatically implies that b'Moadeichem refers to all the Moadim and therefore cannot be learnt the way R. Eliezer ben Yaakov learns it. It follows that R. Eliezer does not agree with R. Yonah's drasha but instead learns that only Rosh Chodesh provides a kapara for the tuma of the Beis Hamikdash and the kodashim.
5. According to R. Eliezer ben Yaakov possibly we can understand better why we say every Rosh Chodesh in Musaf "Zman Kapara l'Kol Toldosam" :- that Rosh Chodesh is the time for atonement. We do not mention a similar thing on Yomtov. This suggests that there is something special about kapara which is only possessed by Rosh Chodesh.
Kol Tuv,
Dovid Bloom