See discussion from 23 March FTF meeting:
http://www.w3.org/2017/03/23-wpwg-minutes.html

How does merchant payment method order interact with registration order from the payment app? There was some agreement at the meeting we need an algorithm to answer this.

Some notes on this topic:

• Related PR API discussion about ordering of payment methods
  w3c/browser-payment-api#481

• If PR API does not define payment method order, then we can probably close this issue but we need to edit 6.1 in the spec (on Ordering of Payment Handlers).

• There is currently no discussion in Payment Handler about ordering of wallet/instrument information based on registration data.

My suggested revisions to the 6.1 sections for consideration...

• The user agent must favor user-side order preferences (based on user configuration or behavior) over any other order preferences.
• The user agent must display matching payment handlers that corresponds to the supported payment methods provided by the payee by user-side order preferences.
• The user agent should allow the user to configure the display of matching payment handlers to control the ordering and define preselected defaults.