he was unable to change the rate due to the Global Shipping Program
Actually, he's right.
Another failure of the GSP.
He could however, invoice you for the item directly through Paypal Send Money.
He should include the eBay transaction number in the invoice to help everyone track what is being sold. When you pay, you are covered by Paypal's Buyer Protection. And he marks the item Paid manually, so that's all good.
The suggestion to pay the GSP price and hope for a refund is .... optimistic... naive....sweet? But then I am a nasty cynical old biddy.
BTW with both your "full price and a refund" and my "direct billing through Paypal" suggestions, the seller would be paying eBay Final Value Fees. That may be what is the sticking point for him.