Hackernews started out as a way for YC to talk to their would-be founders (it was called 'start-up news' originally) and the rest of the postings are the noise and those are the signal. If you are unaware of the relationship between YC and HN you could be forgiven but after more than a decade here I don't think that excuse holds.
Marking job ads more explicitly won't change anything, it is just a way to pressure YC into making some change to satisfy nit pickers and there is far more important stuff to do, and is as far as I'm concerned off-topic given that the question was 'why can't we comment on these postings' and that question has been answered afaic.
Furthermore: the who is hiring threads are there as well for everybody else as well, which given the audience and the fact that these compete directly with YC funded companies should be proof positive that no malicious intent was ever present. If it were then those threads would have never happened.
I think I understand why you are defending HN. You see how a small community grew to what it is now, and all of the unpaid work that went into that. I don't think that is in conflict with the idea of being super transparent (to the point where it's obvious to everyone) about things like sponsored posts. It's clearly not obvious to everyone.
You make a good point about the hiring threads. I agree those are evidence that YC is making an effort to support non YC startups.