PAA, why would the MS not have an issue if he originally assumed the B’raisa was the Rabbonon? The kal vachomer as applied to the case of someone who was taught one halacha doesn’t work (because of dayo) according to the Rabbonon, but according to R’ Tarfon it does work, because the alternative would be to discard the k”v (for that case).
HaLeiVi, there’s a pirush from the Rav on Avos D’R’ Nosson? The pshat you mentioned is found (more elaborately) in the pirush of the Gaon’s brother, but as PAA said, the MS doesn’t agree.