sellisamat The difference is the legal aspect:
3D Secure: The card issuing bank guarantees through the 3DS check that the cardholder makes the payment. If this is not the case, it is liable for the chargeback and has the financial damage.
Apple Pay: The card-issuing bank does not guarantee that the cardholder will make the payment. With a chargeback, bunq the financial damage.
So: Even if Apple strictly identifies the user ... for bunq , payment is legally bunq .
And since we're not talking about regular payments here, but rather fraud, this theoretically high level of security through Apple's identification is only as strong as the weakest link in the chain: deliberate chagebacks by malicious users, weak PIN, poor authentication of certain banks when adding a card on Apple Pay, Man in the Middle attacks, ...