They shouldn't but if you can't have a perfect system then it's best to have a system as close to perfect as possible and that is something we do not have. So ideally an entity wouldn't be punished for requesting a takedown of their own content but because of the insane volume of bogus takedown requests I think it's better to punish those who send them and if anyone accidentally sends a takedown request for themselves then them's the breaks until the system can differentiate between legit, bogus, and self takedown requests.
Furthermore, I'm not sure how YC deleting a post and issuing a DMCA takedown request against content on their own site are the same thing. This isn't about deleting content at all. Whether a site deletes content isn't at issue whether it violates copyright or not. The issue is sending bogus takedown requests to others.