He very possibly would not have, but the point is that someone of authority did come to that conclusion, and once that conclusion was acted upon, we don’t change.
If no justification were found, we might assume that the change was made without halachically valid grounds, in which case we would revert to duchaning (or whichever din we’re taking about).
So minhag does not “trump” halachah, but it is a machria where there is a machlokes, even if without the minhag we would have paskened differently.