Painting bolt heads
If the bolt is supposed to be bare, I have them Black Phosphate plated. There is a place in Stanta Fe Springs (near Los Angeles) called All Black where I take mine. They have to be media blasted first.
For painted bolts I have had some luck with plastic socket inserts or just wrapping the bolt head with masking tape and using a 6 point socket.
I agree that the thinner the paint the less likely they are to chip.
Some of the bolts on the engine, like head bolts, timing cover bolts, and intake manifold bolts were painted with the engine after assemble. In that case, I media blast them before I assemble the engine and do my best to keep them free of oil or assembly lube so the engine paint will stick.