It's instructive though, despite the flaws, and at this point has been replicated enough in different ways that we know it's got some basis in reality. There's a whole bunch of constructivist research around interactionism, that shows that whilst it's not just the person's default ways of behaving or just the situation that matters, the situational context definitely influences what people are likely to do in any given scenario.
Reicher & Haslam's research around engaged followership gives a pretty good insight into why Zimbardo got the results he did, because he wasn't just observing what went on. That gets into all sorts of things around good study design, constructivist vs positivist analysis etc, but that's a whole different thing.
I suspect, particularly with regards to different levels, there's an element of selection bias going on (if for no other reason that what we see in terms of levels of psychopathy in higher levels of management), but I'd guess (and it's a guess), that culture convincing people that achieving the KPI is the moral good is more of a factor.
That gets into a whole separate thing around what happens in more cultlike corporations and the dynamics with the VC world (WeWork is an obvious example) as to why organisations can end up with workforces which will do things of questionable purpose, because the organisation has a visible a fearless leader who has to be pleased/obeyed etc (Musk, Jobs etc), or more insidiously, a valuable goal that must be pursued regardless of cost (weaponised effective altruism sort of).
That then gets into a whole thing about what happens with something like the UK civil service, where you're asked to implement things and obviously you can't care about the politics, because you'll serve lots of governments that believe lots of different things, and you can't just quit and get rehired every time a party you disagree with personally gets into power, but again, that diverges into other things.
At the risk of narrative fallacy - https://www.youtube.com/watch?v=wKDdLWAdcbM