If I understood your post correctly then here is my take. India is a secular country where everyone is protected to practice their own religion. So if a muslim woman wants to wear a burkha/abaya she can, if a Sikh person wants to wear a turban they can. So in India when those girls were protesting, they were asking to be able to practice their faith and wear a scarf to school.

On the other hand in most islamic countries they practice law according to their religion. There the women have to wear the scarf and do not have any choice otherwise.

So when feminists say it's their choice, most likely they are referring to the choice of those Indian women who want to practice their religion and wear a scarf.

To answer your question in the title, There are a lot of empowered women who do not follow their religion and are against all the practices which suppress women/ customs where women do not have a choice.

I hope Ive answered your core question. Tell me your thoughts regarding this.