The libertarian answer would be that government requirements mere represent a necessary
minimum. In any case, it would seem irrefutable that no matter the requirements, there is always room to go above & beyond, and to have such efforts certified by a third party to maximize their use for PR purposes.
In a wild application of signaling theory, certification may even be a useful signal without regard to the actual substance of that certification, as long as it is expensive. Just like a peacock shows his abundance of resources by wasting some of them on jazzy plumage.[0]
I think you’re sort of sympathizing with the airlines here, who are somewhat pressured into spending that, from their perspective, is wasteful: after all, they know they are doing all that stuff they are getting certified for.
I would say (a) don’t anthromorphize corporations—they may be people, but not ones deserving sympathy. And, (b), certification schemes are one of the many often disregarded frictional costs of a market economy. They are unnecessary only in a mythical benevolent economic system that has so far eluded us.
[0] also a good reason to justify flying only with airlines that offer free peanuts.