Bengal was an important part of the Pakistan Movement and, as with elsewhere, the local chapter of the Muslim League got quite powerful during the early 1940s as Congress’ leadership was in jail. Bizarrely, it formed a coalition with the Hindu Mahasabha, the British Raj's leading Hindu nationalist outfit, to take power in the province - I suppose Hindutva and early Pakistani nationalism are pretty similar ideologies, if you ignore the mutual religious hatred.
But there were many differences between the Bengal Muslim League and the Muslim League chapters in UP or Punjab - it used the Bengali language exclusively, and it did not heed to Jinnah’s view of the Muslim community as defined by Persianate culture and the Urdu language. I suppose they could ignore those ideological differences when they were fighting against Congress together, and the Bengal Muslim League heeded Jinnah's call for the Direct Action riots. The last-minute attempt by the Muslim League to create an independent Muslim-dominated Bengal was a recognition of this difference, I guess. But nevertheless, the Pakistan Movement was, if ideologically different, active in Bengal, and so it was only natural to include East Bengal inside Pakistan.
Of course, after independence, the differences between the Bengali majority of the new country and the Urdu-Punjabi elites suddenly became apparent, nearly the entire Bengal Muslim League separated and formed the Awami League, and figures like Suhrawardy went from aggressive Muslim sectarians to nominally-secular Bengali regionalists. But nevertheless, before it the difference wasn't clear, and East Bengal was a very important part of the Pakistan Movement's history.