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You are not right and your logic is completely void. I have been using the same keyboard (Google Indic) for years and the previous version of Onenote android did not have such font issue.
With the same keyboard while I type Bengali in any application like Microsoft word, Google Doc, Microsoft Todo - everywhere Bengali font works. Only in Onenote font breaks.
There is no way to change my keyboard. The issue is in the app and Onenote technical team should fix it instead of bypassing the issue.