The only way for the F dealer to intervene on the lease overage is to buy-out the car before it’s grounded. You can get the payoff and check MMR to compare but I suspect that is a bigger hole to fill than midwest Raptor discounts.
OP will have disposition waived on the MachE for the Raptor purchase. In the past F also extended the W&T waiver when leasing/buying new at disposition (+$750 iirc) - if so may be able to apply to mile overage.
I would separate the Explorer trade and get all the purchase quotes, sell it to the highest bidder / use that with the dealer when trading for the Raptor.