Saying it wasn't been there since the beginning and that supplements only apply to internal damage not usually seen from the outside.
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Well that part is true. A supplement is for (typically hidden) damage found after the car is taken apart.
Unfortunately, this puts you in a difficult position. If you take them to court, they can (note, I didn't say will and I really don't know the probability even though I would guess it is low) have a low-level employee show up with the pictures showing no damage and game over. A Model 3 with cracked glass isn't a unique situation.
It is probably an issue from Tesla, but now that you've had the accident, they will likely deny fault as well. Good luck to you whatever you decide.