Your idea of mesorah is confusing. Is it a way of study? The traditions that are still oral? A secret teaching formula? A code for understanding on your own what was not given over to you? Do you see the pattern. I do. I have seen it a hundred times. It means you can not put a finger on it. So you list the categories that apply to every living doctrine. There is nothing unique about what you call mesorah than what can be found by every philosophical, theological, or anthropological school.
The gemara predates the Mishna. And you should have known that. The Rishonim did not have a tradition on how to study the gemara. That is evident from the writings that they wrote on the mesechta. Any reader notices at once that the authors are working through the basic text of the Talmud. If they were given a certain method, we would see it being employed. To say the Geonim had a mesorah regarding the Talmud, would appear to be correct. Alas, we can discern a tradition at work in their writings. But we can only guess what it was. Obviously, that tradition is lost from us.
We could get into a discussion on Rashi and Tosafos disagreeing in both the basic gemara concepts and their methods of understanding the Talmud. But it would not produce an argument from me that is relevant to this discussion.
I’m not sure what your last line is. But other than societal context, it is hard for me to really parse the opinions of each pair. And I do not know how serious those controversies were. They only are remembered because the other side was also a significant scholar. If it was me instead, I would be considered more yeshivish for it. Like according to the camel is the load line of thing.