The lesson seems to be to anticipate moderators being accused of conspiracy and malice more when you discuss moderator actions. This appears true not just where the stakes are high, like in startups, but everywhere. If you talk about something that may look like special privileges but you know is normal, acknowledge it to save the moderators some trouble. It may deter some of the accusatory comments and give the passerby a more accurate impression.
I agree partly with the lesson but more broadly I think it is that any hint of impartiality//conflict of interest for governing/regulatory bodies will be construed in a negative light. Where I disagree is that you could have saved the mods the trouble. I don't think there was any way you could have worded your original comment, or I mine, or Dang his, that would entirely quell the accusations that followed. There's one person in the thread that continued to insinuate that this isn't a policy or it's a new policy; even though Dang showed his comments about this policy going back almost a decade.
This isn't, IMO, favoritism or protecting YC interests//founders. The thread in question has nothing to do with Lamda, YC, or anything in that regard. It's someone talking about blackhat growth hacking in the open, which might bite them in the ass later. It's a textbook example of HN's stated policy about deletion/redaction in action.