1. Talmidei Rabeinu Yonah (37b of the pages of Rif, DH v'Ein Somchin) are explaining the opinion of the Rif. The Rif does mention Shmuel at all. This certainly suggests that the Rif does not rule like Shmuel. This is also the ruling of Rabeinu Chananel cited by Tosfos (50b, DH k'Man; see Hagahos ha'Bach #4). Earlier in the same paragraph, Tosfos also wrote initially that it would appear that the Halachah does not follow Shmuel since the Gemara states that Shmuel agrees with Rebbi Eliezer, and we know that in general the Halachah does not follow Rebbi Eliezer since he was put in Cherem (see Bava Metzia 59b).

2. Since the Rif does cite the Beraisa but not Shmuel, this suggests that he understands that there is a dispute between Shmuel and the Beraisa. We may now add fact that Shmuel is aligned with Rebbi Eliezer, whom the Halachah does not follow, so this indicates that the only opinion whom the Halachah does follow in the Sugya is that of the Beraisa. If we now also observe that the Beraisa states that one may not lean the plate on the bread, this also seems to differ with the simple way of understanding Shmuel, that one may do whatever he needs with bread. This is why the Rif understands that there is an argument between Shmuel and the Beraisa.

3. The Rif now needs to explain the reason why one may not lean the plate on the bread. He asserts that since this is stated in the Beraisa, it is probable that it is because of the same reason as the other Halachos in the Beraisa. Since the other three Halachos are because one may not do something disgusting with bread, we may say that this is also the reason why one may not lean the plate on the bread.

4. This does not contradict the fact that we never find that Shmuel says one may do something disgusting with bread but he says merely that one may "use" bread, because when one leans the plate on the bread one is not directly doing something disgusting but merely there is a possibility, a "Chashash," that the soup may spill on the bread and this will be disgusting. Shmuel maintains that one does not have to worry that this might happen even though he agrees that if one was certain that it would happen, then he should not do it. In contrast, the Beraisa is concerned about the Chashash that it might happen even though it is not certinly going to happen. The Rif rules like the Beraisa, which is why he maintains that one may not lean the plate on the bread.

5. The above approach answers your question why Talmidei Rabeinu Yonah had to make a new argument between Shmuel and the Beraisa. We asserted that they were merely explaining the opinion of the Rif, who did not mention the opinion of Shmuel. This implies that the Rif himself made an argument between between Shmuel and the Beraisa and ruled liked the Beraisa.

6. Now, however, I am going to attempt to show that precisely because of your important question -- "Why make a new argument between Shmuel and the Beraisa?" -- other Rishonim maintain that in fact the Rif did not learn that there is a Machlokes between Shmuel and the Beraisa, and the Rif ruled like both of them.

(Before we proceed, I want to mention that a short time ago someone pointed out to me that the opinion of the Rif carries significant weight for the Halachah, as the Rambam himself writes that the Halachah follows the Rif in the vast majority of cases. Since the Shulchan Aruch is largely based on the rulings of the Rambam, it follows that the Shulchan Aruch rules like the Rif in most instances. Of course, the Beis Yosef himself wrote that his rule in compiling the Shulchan Aruch was to examine the opinions of three Rishonim: the Rif, the Rambam, and the Rosh, and to rule like the majority whenever there is a dispute between them. This demonstrates to us the importance of knowing what the opinion of the Rif is, and it explains why the Rishonim work so hard in this Sugya to clarify his opinion.)

The Rashba writes that it appears that Rav Hai Ga'on also agrees with the opinion of Tosfos that the Halachah follows Shmuel. The Rashba adds, "v'Af ha'Rif Kasav Ken" -- "even the Rif wrote so," i.e., that the Halachah follows Shmuel.

7. The Beis Yosef (OC 171, DH Amar) explains how the Rashba saw that the Rif ruled like Shmuel. After the Rif cites the Beraisa about the four things that one may not do with bread, he adds that this applies only to acts that make the food disgusting; acts that are not disgusting are permitted. Therefore, the Rif wrote that one may throw nuts, pomegranates, and quinces. The Beis Yosef writes that since the Rif wrote that only disgusting things are forbidden but other things are permitted, it was no longer necessary for the Rif to cite the law of Shmuel. The Beis Yosef implies that since we know that Shmuel maintains that only non-disgusting activities are permitted with bread, it is sufficient for the Rif to state that one may throw food which does not become disgusting as a result. We now know that all activites with food which are not disgusting are permitted. This is the same as Shmuel's opinion, so it is no longer necessary for the Rif to mention Shmuel.

8. In summary, we find that the way the Rashba learns the Rif is the way you understood the Gemara in your question. The Halachah follows Shmuel that one may use bread for all of one's needs, but on condition that it does not make the bread disgusting. Accordingly, we need not say there is a dispute between Shmuel and the Beraisa. Talmidei Rabeinu Yonah disagree with this and maintain that since the Rif made no mention of Shmuel, this implies that he learned that there is a dispute between Shmuel and the Beraisa and he rules like the Beraisa.

9. The Shulchan Aruch (OC 171:1) rules like the Rashba's understanding of the Rif. One may use bread for any of one's needs as long as it does not make the bread disgusting.

Kol Tuv,

Dovid Bloom