In the mishna there is a machlokes how to deal with wine in which there is some yayin nesech mixed in. Tana Kama says that the entire mixture is forbidden to benefit from, but R. Shimon Ben Gamliel (rsb"g) holds that one can sell it for the price of the kosher wine, deducting the value of yayin nesech. The gemara concludes that we pasken that for real yayin nesech we can only rely on RSB"G when barrels of yayin nesech are mixed with barrels of kosher wine, but not on a liquid mixture containing yayin nesech. Whereas for stam yaynam that falls into kosher wine, one can sell even the liquid mixture at the value of the kosher wine.
In the Mishna 49b R. Elazar offers another solution for dealing with bread of issur hana'ah that gets mixed with kosher breads - throw the value of the issur hana'ah into the sea so that you aren't benefiting from it. The Rabbonon disagree with R. Elazar because there is no concept of "redeeming" issur hana'ah. Rashi 49b explains that even RSB"G may agree with the rabbonon who argue on R. Elazar that throwing the value of the issur hana'ah away isn't sufficient, but would still hold that one can sell the entire mixture for the value of the heter that is in it, because by doing so they are not benefiting from the issur hana'ah at all.
The difficulty is that Rashi in our sugya seems to confuse R. Elazar's heter with that of RSB"G. Rashi d.h. chavis (and on 71b d.h. ela), in explaining the position of RSB"G himself writes that you take one barrel and throw it into the sea, thereby permitting the rest. Rashi d.h. v'issurei, explains a similar solution for chometz. Since Rashi himself holds that RSB"G will work even if we don't accept the solution of R. Elazar to throw the value of the issur hana'ah into the sea, rashi shouldn't have used R. Elazar's system to expalin RSB"G?
Perhaps rashi holds that there is a flaw in RSB"G system. We know that one cannot gift issurei hana'ah because the appreciation that the goy will have for you is also considered a benefit. How then can one sell 5 barrels of wine for the price of 4 (deducting the value of the yayin nesech) - he is essentially gifting the 5th barrel and therefore receiving benefit? Perhaps Rashi holds that the solution of RSB"G will only work if one sells all 5 barrels for the price of 5 barrels, and then takes the money of value of yayin nesech and throws it into the sea. Therefore, RSB"G approach is not independent of R. Elazar's throwing into the sea, it is in addition to it. That is why Rashi uses the logic of R. Elazar even in the opinion of RSB"G.