Sam2 and HaLeivi,
A more modern version of this machlokes (on the very extremes) is between the Malbim and the Doros HaRishonim.
I think that the truth lies somewhere in between. One can go through Shas and find instances that support one side or the other. The most likely conclusion is that both are true.
There are times where the Mishna says a stam halacha and the Amoraim argue about the makor (with nafka minas) but there is no machlokes about the stam din in the Mishna. There are further times were the “proto-mishna” says a stam din and later Tannaim argue about its application/meaning/makor. I think that in those instances it is clear that there is a mesorah as to the din and the machlokes is where that din can be derived in the Torah ShebiKsav.
In other cases it seems pretty clear that the Tannaim and Amoraim are deriving new dinnim or arguing on previously held shittos on the basis of drashos.