The intent is that both will always have values, and the values will differ in the iframe case. I would be fine to add a sentence to that effect, so paymentRequestOrigin would become:
This attribute is a string that indicates the <a data-cite="!HTML5#origin">origin</a> where a <a>PaymentRequest</a> was initialized. When a <a>PaymentRequest</a> is initialized in the <a>topLevelOrigin</a>, the attributes will have the same value, otherwise the attributes will have different values. For example, when a <a>PaymentRequest</a> is initialized within an iframe from an origin other than <a>topLevelOrigin</a>, the value of this attribute is the origin of the iframe.
The string MUST be formatted according to the "<a data-cite="!RFC6454#section-6.1">Unicode Serialization of an Origin</a>" algorithm defined in section 6.1 of [[!RFC6454]].
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