kasha-
I know that this is a common opinion. However, there are those who disagree, and this is the opinion of my rebbi and of my rav. And I’m sure you know the Shach himself argues many times on the psak of the mechaber, so even according to him apparently it isn’t so clear-cut.
As for your second point, yes. Rashi argues on the psak of previous generations because of ‘ein l’dayan ladun ela ma she’einav ro’os’, and so did many poskim throughout the ages. As the gemara in Chulin (8a) says, if a Talmid Chacham says a halacha which is a chiddush, even against what was always accepted, we don’t throw him out. That isn’t to say the gedolim who said contrary didn’t have reasons. It’s just that when figuring out the halacha we don’t work with that if it contradicts our logic, because of the principle ‘ein l’dayan ladun’.
One last thing: Obviously by logic I mean a logical conclusion based on the gemara/rishonim, and not simply personal or popular sentiments under the false umbrella of ‘reason’. Such ‘logic’ is nothing at all in the face of da’as torah.