Author of said flagged post here. I agree with you. I wish HN worked such that if a post has more upvotes from high-rep users than flags, that the flags would have no effect whatsoever.
I would personally like that, too. But Dang's bonzai tree that is HN is curated a very particular way which increasingly mostly murders any dramatic posts. I blame Elon, because the Twitter shit really fucked with this site in a way I'd not previously observed. Just another (probably incorrect) theory.
I'm sympathetic in that poor Dang is already grinding it day in and out to keep things afloat, the dumpster fire threads can get out of control pretty quickly and can get ugly and abusive. It's a fine a line.
I wish we could get away with that but one of the dismayingly consistent findings of running an internet forum (or this one, anyhow) is that you can't rely on high rep for almost anything.
I wonder if there's any good way to avoid the vetocracy-like effect then, where a small number of users who don't like a post can effectively bury it even if a much larger number of users do like it.