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When you link a passphrase with a pin, your passphrase is used right after you type it into the device to alter the master key derived from your seed words into a new master key that is associated with that pin.
Then the passphrase is forgotten, but that doesn’t matter anymore.
The master key from which all private keys are derived is what matters.
As you may have noticed, not all wallets do this.
Other wallets make you type it every time and it’s kind of a pain, or at the least, it does not encourage the use of a long/secure passphrase.
Some wallet makers actually market having to type your passphrase each time you use it as a „feature“ that mitigate their devices‘ vulnerability to physical key extraction attacks.
But really it’s just piling on a bad user interaction flow on top of a weak hardware design.