@Udaya Kumar Thank you for reaching out to us. Your assumption is right, MFA has no relation with 40K MAU. A flat fee of ₹2.487 is billed for each SMS/Phone-based multi-factor authentication attempt. You can leverage Azure pricing calculator for the same [https://azure.microsoft.com/en-us/pricing/calculator/
As an alternate option you can use authenticator app instead of SMS/Voice.
Let me know if you have any further questions, feel free to post back.