Perhaps the Gemara is alluding to the fact that Rebbi does not actually permit doing anything that is Asur d'Rabanan on Shabbos during Bein ha'Shemashos. His authorization is actually quite limited, as we discussed in our Insights to Eruvin 32 (copied below).

Best wishes,

Mordecai Kornfeld

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3) DO THE PROHIBITIONS OF "SHEVUS" APPLY DURING "BEIN HA'SHEMASHOS"?

QUESTION: The Gemara quotes Rebbi who rules that the prohibitions of "Shevus," or the Isurei d'Rabanan of Shabbos, do not apply during Bein ha'Shemashos. Rebbi's ruling is recorded as the Halachah (SHULCHAN ARUCH OC 307:22, 342:1).

If the Gezeiros d'Rabanan do not apply during Bein ha'Shemashos, then why does the Mishnah in Shabbos (34a) state that it is prohibited to immerse utensils in a Mikvah or separate Ma'aser during Bein ha'Shemashos? Those acts are prohibited on Shabbos only mid'Rabanan. Does Rebbi argue with that Mishnah and permit those acts to be done during Bein ha'Shemashos?

(a) The RITVA cites the RA'AVAD who explains that Rebbi certainly agrees with the Mishnah in Shabbos. Rebbi's ruling that the prohibitions of "Shevus" do not apply during Bein ha'Shemashos refers only to the laws of Eruv Techumin. Rebbi states that when the Rabanan enacted the laws of Eruvei Techumin, they declared that the Eruv is valid as long as there is no Isur d'Oraisa which prevents the person access to the food of his Eruv. If there is an Isur d'Rabanan that prevents access to the Eruv, the Eruv nevertheless remains valid. However, the Rabanan did not actually permit one to transgress an Isur d'Rabanan during Bein ha'Shemashos in order to get to the Eruv. (This is similar to the concept that Rashi mentions later (end of 32b) when he says that the area of a person's Eruv Techumin is considered like a Reshus ha'Yachid that extends up to the sky, even though it is not really a Reshus ha'Yachid.)

(b) The RAMBAM (Hilchos Shabbos 24:10) writes that one is permitted to transgress an Isur of "Shevus" during Bein ha'Shemashos for the sake of a Mitzvah. Since an Eruv is made for the sake of a Mitzvah (such as to learn Torah from a teacher who is farther than 2000 Amos away), one is permitted to do an Isur of "Shevus" for that purpose. Rebbi agrees, however, that one may not separate Ma'aser from fruit during Bein ha'Shemashos, since one does not separate for the sake of a Mitzvah. (MAGID MISHNEH ibid.)

(c) RASHI in Beitzah (19a, DH Meida Yada, according to the MAHARSHA there and SHA'AR HA'MELECH, Hilchos Eruvin 1:22) explains that even during Bein ha'Shemashos, one may not do an act that is not needed for Shabbos at all. (For this reason, one is prohibited to immerse a utensil in a Mikvah during Bein ha'Shemashos in order to purify the utensil for use with Terumah. Since the utensil will become permitted to use for Terumah only after sunset following Shabbos (at which time the utensil becomes fully Tahor), the Tevilah is not an act that is needed for Shabbos at all.)

Accordingly, this might be the type of Tevilah that the Mishnah in Shabbos (34a) prohibits. The same rule applies to Ma'aser during Bein ha'Shemashos. If one will not eat the food on Shabbos (for example, it is raw at the moment, and it is normally eaten cooked), one may not separate Ma'aser from it during Bein ha'Shemashos. (See also Insights to Beitzah 19:1.)