Well, there is no single answer for your question basically. An social scientist or an Anthropologist may be in a better position to answer that or even a Islamic scholar could be a choice.
At least I could give you some direction of my thoughts. First Islam and Local community culture is not mutually exclusive. You can have both. Also you are wrong in identifying 1947 two nation theory as being just a religious division. But in fact it was just a economic segregation between Muslims and Hindus where Muslim wanted more participation on Political and Economic affairs. Muslim did not get separated from India because they could practice more Islam in their new country or they could make that a fanatic Islamic country. You need to study Jinnahs words closely. Also I needed to mention Fazlul Haque, you need to study him as well and pay some attention to political and economic affairs in early 20th century, not just after 1942 onward.
Why worry about Indian Bengali as they are on the other side of Border? Depends what kind of worrying you do for them. The reason I am worried because they are also part of our heritage and culture. they read our books, they feel proud when Dr. Yunus got Nobel prize, they celebrate or 21st February, they celebrate our independece day and so on!!! They also work as a buffer between huge India and Bangladesh. India can never wage a one sided war keeping all those Bengalis on their soil. Remember 18 BSF got killed by BDR and there were wholesale protest in India but west bengal, where People in west bengal sided with Bangladesh and said that piece of land (seemed to them) as part of Bangladesh. When India try to push in Beggars from their street in Banglades, West bengal is the one there to protest. Also let me remind you that, Bangladeshi offered India, only to deploy Bengali BSF on indian side? Why is that? Because Bengali BSF will not open fire to another Bengali even though they are on the other side of border.
Also some of the people try to suggest that All the muslim Ummah should belong to the same country. Thats a blunt reasoning as Islam was never meant to be confined in the same country. Since the time of Khelafat, there were different country created, country merged and so on!!!