If i am painting a car and putting the bolts in later its because i am using stainless normally and its not a stock type resto, sometimes i use bolts painted a different color and have to touch them up after they are tightned up.
on a stock resto type paint job i paint the bolts allready on the car like the factory did. i would spray some paint on the fender where the bolts go before i put the bolts in just so there is some paint under them then put in the bolts and paint everything and clear it.
most of the stuff i paint is not factory so i paint it with the bolts out of the car and a lot of times use stainless bolts , then there is no paint to scuff on them when they get tightened and they look nice.