Edit: oh - I think that one was actually marked a [dupe] by software. I'd need to double check this, but if so, it's because it interpreted the link to the other thread as a signal of dupiness.
Edit 2: yes, that's what happened. When a submission is heavily flagged and there is a single comment pointing to a different HN thread, the software interprets that as a strong signal of dupiness and puts dupe on the submission. It actually works super well most of the time. In this case it backfired because the comment was arguing the opposite.
You're right that most such software tricks, especially anti-abuse measures, need to be secret in order to stay working.
Of course, do not attribute to conspiracy that which can be attributed to a bug! ;-)
How easy it would be for bad actors brigading with freshly created accounts, or not-so-freshly created accounts with a history of brigading, to abuse this feature to censor stories?