Authors are persons and clearly have freedom of speech, no one here is arguing with that.

I believe your argument is that, because the author of a NYT piece has the right to free speech, any law prohibiting the NYT from publishing that article is invalid. Not because the NYT has a right to free speech, but because one can "fall back" on the protection afforded to the original author.

Doesn't this same protection apply to the author of an advertisement published by a super PAC?

The NYT shouldnt need to be involved in the discussion, they are simply making the free speech of an author available to more people. A bit more complicated megaphone.

Someone working for a super PAC how ever isnt spending his own money.

Sure ... but does the New York Times Corporation have freedom of the press.

US law had always interpreted media companies as having the freedom of the press (but not necessarily freedom of speech).

Corporations may or may not have freedom of speech. But it would be bizarre if a media company didn’t have freedom of the press.

I don't see what freedom of the press has to do with the article or with my point.