I heard in a Shiur, never saw inside, that Reb Ashtori Haparchi says that there are things which we do that are Neged Hatlmud. Living in Mitzraim is one of them. Maybe PAA will get us the pertinent quote.
Also, Tosafos famously writes that there are things that ‘we’ do that are from Sfarim Chitzonim (i.e. Meseches Sofrim). In these cases it is the Mesora that ruled.
The Mesora is more of a decider than a Mechadesh. I think this is where Sam is taking things the other way. Mesora is when Klal Yisroel Paskened a certain way. By definition, you can’t find the later Hachra’a in the earlier words.
You are referencing those who changed and were Mechadesh as a symptom of not changing and following the accepted view and Psak.