If it hadn't been a 200 km stage, DQS would probably have gone for a bunch sprint, and maybe also if the break had been brought back, but with Ballerini up there they can now relax, since Matthews won't score any points either.
Of course it's also possible that Merckx either managed to spook Cavendish earlier or decided to pay him that increased salary, Cav's been looking for, out of his own pocket. We'll know that for sure, if Cav fails to overtake Mørkøv in the last meters on Champs-Élysées, because he drops his chain too early for once.