I don't think crypto will work here for a few reasons.
1. PaymentMethodData:PaymentMethodIdentifer is a 1:Many relationship
Each PaymentMethodData object in a payment request is has a sequence of payment method identifiers. This is by design, because it's possible that a merchant may wish to group the data they provide under a set of payment methods for which the data is common.
2. Not all payment methods will easily support PKI
What would the public key for the basic-card payment method be, for example? We have reluctantly agreed that for "proprietary" payment methods we require a payment method manifest that defines some details (such as allowed payment apps) to be hosted by the publisher of the payment method. To expect that entity to also host public key infrastructure seems like a tall order.
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