Yes, that's one of three things that HN gives back to YC in exchange for funding it. The other are job ads and Launch HN threads. This is in the FAQ: https://news.ycombinator.com/newsfaq.html.

I can't speak for everyone but with the volume of investments YC makes, I find it hard to be biased toward a YC company.

I was told the reason for the orange username was so that we didn't start a fight with other YC alums, which would have been awkward back when the community was only a few hundred people.