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You can throw away the seed that Metamask generated. Unfortunately it’s just a design decision by Metamask that they force you to create a software seed phrase before letting you also connect a hardware wallet.
(But actually I’d also save the Metamask seed somewhere just in case you accidently send some assets to that account, so you’d have a way to recover those. But in normal use, you should only be sending to the Ledger-linked addresses)