The TouchID is bound to a device - of course, I could copy my secret into a secure enclave that is only accessible through TouchID. Could even just store my GPG key there. With a Yubikey, I generate the key on an airgapped device and store it on the Yubikey. No other piece of hardware ever needs to see my secret key in plaintext. I could achieve the same with TouchID, generate the secret key inside the enclave, but then I cannot move the secret keys out without some other computer baring witness to that.

I really do not want to give Apple any more leverage over me, I'm looking to minimize it.