First, I want to comment slightly off-topic about how your post was somehow surfaced on my Google feed. It really is amazing how much Google knows about us, even about the Apple products I use.
Unfortunately, I have been in the exact same situation as you, but even more unfortunately mine doesn’t have a happy ending.
I bought my 15 inch 2016 MBP around April. I originally bought one around Christmas. I had never owned a Mac before, and after seeing the announcement I decided to try one out in store. I loved the keyboard, and really wanted to get something with a bigger screen, as my notebook has become my only computer. So, despite the immense costs I pulled the trigger. After some time with it though, I just couldn’t justify the costs, and returned it.
Then, around April, Apple started offering refurbished models. The discount made the price a bit more reasonable. In addition, I had picked up way more work, so I really wanted more screen. And the keyboard! So, I picked up the 15 inch refurbished model I’m working from right now.
Since April, I’ve been travelling non-stop nearly. But, nearly as soon as I received the computer, I noticed the exact same noises as you. Clicking, popping, sometimes alarmingly loud. They can happen randomly, or when adjusting the screen. They are especially noticeable when the computer has cooled down for a while, and you open the lid. It probably cracks or makes a loud noise >50% of the time when opening the lid.
When I settled down, I was finally able to take it to the new Apple Store in Taipei, Taiwan. Just like you, it was a long commute from my house. It was also completely useless. First, they tested it in the middle of the shop. Loud, full of people, with music playing. How could they possibly hear anything? Eventually, they took it behind closed doors, stayed there for a long time, then returned and told me there was nothing wrong.
Yes, they essentially told me that I had purposely travelled an hour and a half for no reason. The only thing they could do was ‘hold it’ for further testing, which they gave a typical 1–2 week window. That was of course, if they actually found something wrong, which they told me there wasn’t anyway. I didn’t waste 1 and a half hours for no reason. I have a spreadsheet of how frequently the noise occurs, and video evidence.
For now, I really don’t know what to do. I’m located semi-permanently in Japan, where I haven’t tried getting service, but I’m worried the service will be the same as in Taiwan. Ideally, I would like to try the original shop it was bought at, in Vancouver, but that is a long trip.
Seeing your post gave me hope though. It seems that there is actual acknowledgement at Apple that this is a real issue. Maybe I will try it in Japan, though the chances of them knowing about it here seem quite slim.