On the plus side, I'm very happy to see that YCombinator decides to send, not just a rejection, but actionable feedback that they think the company should follow. I think that's a good thing, and so far samples of these have seemed to usually hit the mark.
On the other hand, the reason they always tell you never to explain why you gave a candidate a "no" is, that it will give them grounds to think you are wrong and discriminated against you. That might (might!) be the case here - the Author seems to give serious weight to the possibility of discrmination, which is of course completely possible. Had YC kept their mouth shut and not offered their valuable advice, maybe there would've been less thoughts of discrimination? I'd just hate to discourage YC from offering advice.