I'm not sure they put too much thought into designing these doors/windows. For the Model S, for example, the windows do the same, go down a few cm but they don't actually push up into any seal. When the door is closed, the window just pushes very slightly against the seal, doesn't go in/under at all. The door would very easily open if the window didn't go down at all.
On the other hand, maybe the windows go up/down when the doors open/close, so they doesn't get forced either way because of the sudden pressure difference?