I need to write the whole piece about this, but the thing to understand is that the NYT is now just Facebook. The platform dictates narrative to normies, is totally gamed by the right, and is still so ubiquitous as to be unavoidable even by those who see how broken it is. It's just Facebook.
What I think we saw during and after 2016 was the Times re-understanding itself as An Institution first. Institutions have different priorities around risk and survival, and that perspective explains a lot of otherwise baffling and out of character behavior.