You shouldn't see anything change, because we haven't been subject to editorial pressure in the first place. The job ads will still be a thing but in my mind they're off to the side. We're not going to open them to comments because HN comments are for discussing intellectually interesting stories, which job ads aren't—they're job ads.
If you want to make claims about preferential placement (and yes I realize you're just saying "appears", but still, people are quick to believe these things), I'd appreciate concrete links so we can look into them. We try hard to be even-handed and when there are marginal calls, err on the side of not playing favorites.
YC founders and current/former employees are a large and valued part of this community, stories about YC startups often are interesting (by HN's definition), and lots of HN users like to follow them in particular, so of course you'll still see plenty of YC-related stories on the front page. It would be weird not to. Of course those stories are subject to upvoting and flagging as much as the others are.