I was especially able to determine root cause when driving on a long trip as it became irritating whenever the road surface was not perfectly smooth. So either the seal there was too stiff or metal behind the seal that is causing the squeak of the window on the seal.
I tried removing and re-seating the top part of the driver's door seal and also talked to support. The consensus was that rimless windows are subject to this. Well, I have 2 other cars with rimless windows, my GT-R that is 11+ years old, and therefore has gone through 11 winters and summers, does not exhibit any of these problems. The seals on the Model 3 seem rather stiffer, compared to other cars.
So the solution ended up applying a liberal amount of Gummi Pflege Stift at $12 from amazon to the door seals in multiple locations.
The key to stopping window squeaks in Model 3 |