Sounds like those are 1/4 in. "body bolts". By definition, body bolts are painted body color. See:
https://board.moparts.org/ubbthreads/show...e=2#Post7372056The finish from the bolt maker was, as described by amkproducts.com, "S2 Phosphate & Oil (gray - black)".
Phosphate & Oil should be the same as Parkerizing plus oiling, the gun metal finish on military weapons since about WWI. Chemical kits are sold by blacksmithing suppliers and relatively easy to DIY but maybe not economical for a only a few bolts.
Besides, body bolts were typically S2, then painted with body color; therefore the S2 mostly never shows. Better to just clean them up, remove the "oil", and paint them body color, same as was done at the factory. Unpainted S2 bolt heads on painted parts does not look right.
Absolutely everything that was body color, the body shell, all body panels, battery tray, hood hinges, trunk hinges, door hinges, grille valences, etc., were bolted up and painted as a unit, including the bolt heads.
On my car the yoke cross member bracket, hood pop-up spring, hood lock vertical support, and the upper and lower grille panels were all bolted to the car with 1/4" bolts then painted body color.