I work at a Ford dealership, in the collision center, and have had similar questions asked all the time. First of all, the repair was under warranty(?) if it doesn't match (refinish) tell the dealership to fix it. Yes the repair will always be tied to the truck through Ford OASIS but I highly doubt it will cause any resell issues regardless where you sell it. I'll agree the best course of action is to talk to the dealership and ask them why it wasn't mentioned and see if they'll do anything to make the situation better... Personally, I wouldn't do anything other than verify color and fit (they probably blended the door too)