First off the fact soemthing is different then the Mesorah does not automatically diqualify it.
It does mean that you need really, really, really big people who know the entire Torah and have reached the status where they are generally accepted to be Gedolei Yisroel to change it.
In the time when Beis Yackov was started there were many against precisly becuase it was against Mesorah.
Gedolei Yisroel at the time, led by the Chofetz Chaim and the Gerrer Rebbe, approved it as such it was implemented.
I do not see any Gedolei Yisroel of our time approving of this practice.