Why is a sefeik sefeika permitted? One possible explanation is that the Torah or chachamim only prohibited a safeik, but a double-doubt is too far removed and was never included in the issur. A second approach is that really every safeik should be assur, but a safeik sefeika is permitted because there is a rov l'heter, e.g. if I have a 50-50 chance of heter vs. issur, but even the 50% issur is really only itself a 50-50 safeik issur what that really amounts to is 75 heter vs. 25 issur.
Rabeinu Tam may subscribe to the rov theory of sefeik sefeika, so when mixture #1 falls into mixture #2, I have a super-rov, or sefeik sefeika, which Rabeinu Tam does not want to find a braysa prohibiting. The Rivam may see rov as a different category completely and therefore a double mixture is nothing more then a giant rov which has nothing to do with sefeik sefeika.
Alternatively, when a mixture falls into a mixture, while there are 2 seperate sefeikos being raised (hence R'T says this is a sefeik sfeika), the underlying nature of both questions is the same: is the issur in this ta'aroves? Does sefeik sefeika focus on the number of questions, or the nature of doubts being raised? Perhaps this is why the Rivam calls this a double-rov and not a sefeik sefeika.