Because it is illegal to change the VIN. The V5 is not the same as the VIN of a vehicle.
The VIN plate on the car will always say "202" for a black car out of the factory. If that black car is sprayed RSP, it would still have to read 202 on the VIN. The V5 will say "blue", but the VIN will not.
I didn't say it would lower the value, I said it wouldn't be worth as much as a "from the factory colour". It depends how picky you are. Personally, if I was buying a TT6 Supra I'd want the colour to match the VIN, as it would (if everything else remained stock) appreciate better than one with a colour change.
That goes for any big change though (bar single conversions etc)
An auto to TT will not appreciate like a factory TT6.
A TT6 out the factory will apreciate better than one with a colour change.
Just my opinion, but I'm sure many on here would agree.