Any cost over runs are borne by the manufacturer, NOT the government. Any equipment that does not meet spec must be redesigned/modified to meet spec at the cost of the manufacturer, not the government. Boeing is going to lose a LOT of money on this contract.
Boeing may lose money on the $4 billion EMD contract (the only contract so far awarded), but it will make this back in spades on the full-rate production contract. If it were any other way, they would simply pull out.