From my experience, as I killed the battery the first night I had the car home, it is not a big deal.
The windows push up into the rubber to provide a more airtight seal to cut down on wind noise. I dont' think they are actually up into the body. They should flex enough to just open the door. I know that BMW and Mini is similar to this.
If anyone disagrees, let me know. I'm always interested.
J
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