Let me elaborate. He won the auction of the item but wants to pay for the item not through eBay because his "app" on his mobile needs "updating" and won't let him finish the transaction on here.

As long as he won it through eBay that is what matters = you are paying your FVF.  How he pays is totally irrelevant to eBay; people can pay cash on pick up, by DD or  by PP.