Guys, I posted about this exact same issues in another thread here titled "iPad Clicking Noise" just the other day. Mine made noises within hours of me taking it home and it's as though here is too much play behind the screen or that the adhesives inside had come loose.
I went back to the Apple Store and got a replacement unit which has been silent since. It's been 2 days since I did the swap and that's no signs of the noise. The Apple Store employee had no issues as I was within my 14 day return window. He even said to come back again if this one makes the same noise. So don't hesitate to exchange yours out if you just purchased it. My new unit was also made in the same week as the clicking one in the same factory cased on the serial numbers. So I guess it comes down to luck of the draw just like getting a good LCD panel.
As an aside, iFixit did a 12.9 IPP Teardown video on the 2016 and there appears to be a spacer on the WiFi models, where the antenna bands would be on the cellular ones right BELOW the front facing camera. I am wondering if that has anything to do with it. There doesn't appear to be any videos of 2017 12.9 IPP teardowns yet so I can't confirm if they are the same internally. Its food for thought.