What they say is that they don't respect pseudonyms in stories unless there's a compelling reason to do so in that particular case. There appears to be a political bias to the exceptions, but good luck getting an editor to admit that even to themself, let alone to others.

There can be a difference between having reasons and being able to present them. Humans are known to take cookies from a cookie jar when nobody is looking even if nobody says "I take the cookie althought I am not allowed to". Even young people know to try to spin it somehow. People will not call themselfs villains but there are villains in the world.

In a situation where your stance is indefencible staying silent might make you more credible than making a bad defence.

Thus it might matter more whether both sides have had opportunity and effective means to express themselfs rather what all sides stories are.

In the case of a an actual policy it could also be that multiple people compromise to uphold the standard and different parties have different rationales for defending the standard. Then it could be that there is no rationale because there is no unified decision making process behind it.

NYT hasn't made a public decision to actually publish the article, so there's not really a situation for them to make a public statement about the individual case. 

if by some malicious people you're including people at the NYT who view controversy as a good thing as a proxy for clicks, yes.

We can remove duplicates. Thanks for highlighting.