I think Emptywheel is right. And recall that Rudy Giuliani has pretty much said that his job is to defend the president against impeachment.
If Mueller is following that DOJ guideline which says that a sitting president can't be indicted --- and everything about him suggests he's playing it all by the book --- then he's not considering the president a target. He caught himself in the interview and the NY Times mischaracterized it.
Remember when Trump denied that he knew anything about the Stormy payment?
Note the tone of voice. Well, in that NY Times interview he adopts exactly the same tone when he says this:
HABERMAN: “Did you ever talked to him about Wikileaks?
TRUMP: “No. No. I didn’t. I never did.”
HABERMAN: “Did you ever tell him or other people to get in touch with him?”
TRUMP: “Never did.”
This is a tell. It's the tone of voice you hear from a five-year-old with chocolate all over his face denying that he ate the candy. All innocence, brief and breezy as if he hasn't a care in the world.