This issue was discussed at the F2F.

The discussion suggested that we should support merchants specifying a preference and allow users to express a preference that overrides merchant preferences.

In TAG review @triblondon said:

#23 and #4 discuss the ability for merchants to express a payment method preference and to charge differently for different payment methods. Merchant preference seems basically meaningless unless there is a charge element - the user has no reason to choose a particular payment method simply because the merchant wants them to, but they would certainly be swayed if using one method added a surcharge. Perhaps the simplest way to model that would be to have the merchant pre-calculate a supplement charge to attach to the payment method at the PaymentRequest level, rather than polluting the PaymentDetails items dictionary with multiple additional charges per item (this is suggested in w3c/browser-payment-api#4 (comment), which I agree with). I'm concerned that any potential desire to add granularity to the cost of an individual item will get multi-dimensional very quickly - eg supporting different charges based on payment method, and also expressing pricing in different currencies, you would need a value for each intersection of that possibility space.