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the reason why the Basmalah should not be recited at the beginning (of al-Tawbah) is that it came with the sword (i.e., the command to fight the kuffaar) and it exposes the hypocrites and their foul deeds in a manner that is not unlike any other soorah, and this theme is repeated throughout Soorat al-Tawbah.
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That's the reason there. And Bismillahi Arahman Araheem means, in the name of God, most beneficent, most merciful.
An example is when we slaughter an animal, cow, sheep, chicken, etc. We don't say Bismillahi Arahman Araheem, because this isn't an act of mercy. When slaughtering an animal we just say Bismillah wa Allahu Akbar.