He's not an employee of the NY Times, per se, though, and I don't think he's bound to their reporter's rules. He licenses the 538 brand to the Times (similar to the deal Freakonomics got).
Small pet peeve of mine -- "per se" means "in itself". So, if you read back your sentence, "He's not an employee of the NY Times, in itself", you'll realize this is an improper usage.
It's popular to mis-use "per se" when you mean "necessarily", as in, "she's not my girlfriend, per se", but this is not correct, either. I expect this is how you meant it -- "he's not really an employee of NY Times, he's more like a contractor".
Here's an appropriate use of "per se":
"An aggressive psychological interrogation, per se, is not torture. It only becomes torture when it causes physical harm or lasting psychological trauma to the prisoner." <-- note, this is just a language example, not a statement of my position :)
I think whatever the relationship, it's clear he no longer comments on anything that isn't directly poll-related. Someone is telling him to "stay in his lane" and he's doing it. His pieces are all long, detailed poll analyses.
Nate could be pretty hilarious in print. I want the old short snarky articles back.