However, South West Airlines who wrote the $1m per airframe penalty clause appear not to have received even a glancing blow?
Southwest was just a customer seeking a deal on a product, Boeing said yes we can do that, so the airline bought in. The longitudinal handling issues required them to do something to alleviate the problem and after trying aerodynamic fixes, which didn't work, Boeing came up with MCAS. SW are not in the aircraft design business, they just say as a customer what they would like, it's up to the manufacturer to tell them what's possible. SW made an offer, Boeing accepted, same as when you walk into a car dealer.