We don't know what's going on. Maybe Patek hasn't determined if the watch is actually a manufacturer defect. And maybe once they did, they'll cover the shipping charges. All we know is that the watch has been dropped off and a shipping charge was charged. So there's still a chance that Patek will ask the shipping charges to be refunded.
A store isn't able to make the determination of a warranty defect. Thus, a store should charge the shipping fee. Let's say the store didn't charge a shipping fee, and now Patek says the watch isn't a warranty defect. Now the client has to pay both the shipping fee and the repair fee. The store shouldn't make any assumptions and charge the shipping fee.
Also, I dug out my copy of the Patek Philippe guarantee. And the clause that is applicable here reads like this: "The Guarantee covers all manufacturing faults and material defects as confirmed by an Authorized Patek Philippe Service Center only." So the watch has to go to a service center. NOT a boutique. So, our poster is halfway there, but not all the way there. So a store/retailer/boutique is perfectly right to charge a shipping fee.