The Chazon Ish wrote that the rulings of the Mishnah Berurah are like rulings by the Sanhedrin in the Lishkas Hagazis (Igros Chazon Ish 41). I don’t see how Rav Schachter can make his claim.
Also, the M”B has been accepted, in fact, as, in most cases, halachah l’maaseh, whatever the reason, so trying to change that by arguing that he changed the halachah doesn’t seem to make sense.