1; Most cars will lose their factory livery. You can attempt to recreate it, but the decals will be low quality compared to buying the car in the default color/livery combo.
2; OCD time but doing that and you'll lose the color code displayed in your garage.
3; Not all factory colors are available under the real car paint option anyway.
To me 'repainting' it is just a low-effort workaround for a shoddy system to begin with.