On Temurah 20a, the Sfas Emes explicitly resolves the puzzle of why the halacha follows Rebbi's opinion over Rabbi Shimon's despite Rebbi being described as a lone dissenter deciding between them, by tracing the dispute back to the underlying machlokes in the mishnah between the tanna kamma and Rabbi Shimon over whether an animal may be sold without a blemish, and concluding that since that mishnah presents a plain dispute of an individual against the majority, the halacha follows the majority (Sfas Emes al HaShas, Temurah 20a).
This is consistent with the Sfas Emes's broader approach elsewhere in Temurah, where he explains that the Rambam rules like the Chachamim rather than like Rabbi Shimon precisely because the Chachamim are described in plural language against a single tanna kamma, reinforcing the principle that an unqualified plurality outweighs an individual opinion (Sfas Emes al HaShas, Temurah 18a).
The Sfas Emes's broader method of tracing a later halachic ruling back to its root in an earlier mishnah's dispute, rather than taking the later Gemara's stated reasoning at face value, appears again in his treatment of the deduction from Rava's statement about consecrating a male animal for its value (Sfas Emes al HaShas, Temurah 19b).