What are the benefits of Secure Element in Hardware Wallets?
- Seed words never leave device but they stay in Secure Element
- Secure updates
- Generating 'random' numbers
- No tempering
The mnemonic code (which you are referring to as "seed words") are not stored on the secure element.
The actual seed is stored there. The mnemonic code is only used to generate the seed.
If that were true, it would be possible to add a passphrase only during the input/generation of those 12(24) words. But at least in Ledger I can add a passphrase whenever I want.