I don't disagree with you whatsoever. It definitely felt more organic to me because I follow a lot of the Obvious Corp. folk on Twitter, but I think it's naive to think that any major tech-focused publication (and I'm being broad with the definition of publication here) doesn't specifically submit stuff to HN.
I have no idea how HN's ranking works, but I wish there was some sort of diminishing return bias against a given top-level URL.
I dislike Medium consciously, but not for the reasons you present. I dislike the site because I don't think its prominence here in HN was progressive, but rather very sudden (one month it was nothing special, and the next one it was always on the main page).
That tells me that either Medium is the website to end all websites, a site so popular that it took news sites by storm and whose news cannot be ignored, or that their marketing team is artificially pushing their content in HN to gain views. The fact that they have a main page article discussing how awesome the site is doesn't help either.
Of course, I have no evidence whatsoever of this, but that's how it feels for me. So as suggested by a fellow HN commenter, I just ignore everything from them.