To be fair, it is disclosed on the FAQ page:
Another kind of job ad is reserved for YC-funded startups. These appear on the front page, but are not stories: they have no vote arrows, points, or comments. They begin part-way down and fall steadily. Only one is on the front page at a time. The rest are listed at jobs.
I don't know where else they would disclose it, the fact that you can't vote or comment on it clearly shows you it's different. It's way preferable to e.g. astroturfing, and is not a dark pattern a la Amazon tricking you into prime