2 points.
If you choose to send your child(ren) to a particular school and they have specific rules, you should keep those rules.
If your kids are not in a particular school and a Rosh Yeshiva states in his opinion and it is contrary to what your particular Rav/Posek tells you to do, then follow your own Posek. I would assume that your own Rav/posek is aware of the statement of the Rosh Yeshiva in question and chooses to issue his psak anyway. even if he is not aware, it is his Daas Torah that you are following.