Dy I was thinking about it and the truth is the m”a you cited how’s there IS such a thing as “minhag over halacha” granted it doesn’t apply to ANY act that a person describes as a minhag. However the concept is real and while there are individual rabbonim who would reject it’s application in some examples brought above, we COLLECTIVELY would apply it in every single example brought.
Even the sukkah example WE don’t equate not eatingeating in sukkah on shemini atzeres with not making a seder on the second day pesach (the most analogous example I could think of that involved a mitzvah aseh). Even if a rav paskened that they were the same, obviously we collectively don’t view them the same, rather we allow and even respect (I believe you used that word) the fellow who eats indoors for following his minhag even though it is against halacha, since it is in compliance with the m”a.
I can’t think of any example of a (actual) minhag that wouldn’t meet the m”a criteria.
Another example that came to mind was not wearing techeiles. We come up with all sorts of tenuous reasons to justify our minhag, as we should! It doesn’t matter what halacha says we follow our me sora which sadly was lost. Of course we need some justification to be in compliance with the m”a’so criteria so we come up with a justification.
The bottom line is: the m”a shows clearly there is a concept of minhag trumping halacha. Though with an important caveat that (almost be definition) doesn’t exclude any actual minhag