I think you're looking at this too negatively, either that or you just don't like realism, which I thought you did because of the headlight thing. This is a very realistic approach. I agree that the mod shops not being there do suck, but like totalaccessGTA said, Niko is a low profile criminal, if he goes around with a car with a red paintjob with shit all over it and nitro and a spoiler, it's not to discreet.
I see your aprroach BUT ! In real life you can do what ever you want to your car/truck/bike so it is a downgrade.
You know i thought RockStar was smarter than that!
BUT! Cops aren't that stupid to let you walk a free man when your car is a different colour
And you need to let the paint set dry before you drive off
dude your talking to a body shop owner that puts trucks 1 foot up in the air on big 44" tires!
NO SHIT It should stil be in the game!