SOLUTION:
I had the exact same scrunching/chattering/rattling problem on my new 2018 BE that's only 6 weeks old. I tried a bunch of different homemade fixes but finally got fed up and brought it to the dealer.
During the first (unsuccessful) attempt they replaced the window channel. The theory was the window wasn't seated properly so a new channel would hold it more securely.
A few days later I picked up the car drove it around the corner, and right back to the service area. It wasn't fixed - still scrunching? Really frustrating because I was so explicit in my description. I even left type-written instructions in the truck with pix, color coded arrows, etc. This forum made me realize this was going to be a tough one so I was trying to be as detailed as possible.
After a little complaining (truck only has 700 miles on it!) the "sound" tech came out for a diagnostic drive with me. In the beginning he played dumb but eventually he heard it - probably because I was so adamant about pointing it
Luckily, the tech was good, took me seriously and had me schedule a second appointment. I picked up the car yesterday and the rattle/scrunching sound is gone!!!! I'm so happy!!!
The invoice said they replaced the "driver door cap and sash garnish". Basically they replaced the rubber seal and the triangular plastic cap towards the lower front corner of the window.
For everyone's reference here are the part #s:
72315-TG7-A01 SEAL
72496-TG7-A01 GARNISH
Hope this helps.
Good luck!!!