I experience it as well, like the color of the AE86 is default as black, apparently I already change it check some prints on paints. now for the full color of the color its self is the original first version of the AE86 all white upper body (hood) but for the latest AE86 where takumi got the car already that bunta his father gave it to him, the hood is already black when its all modified on the latest story of the Initial D. please see link below.
I have basically the same bug as QBertt, When i get into the game, and bought the car, it uh...well it looked like it came from hell, it's all black, the stance is super weird, and it has no tail lights or headlights.
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https://www.drifted.com/initial-d-ae86/
image: https://steamcommunity.com/sharedfiles/filedetails/?id=2920246227