The bolts are not visible from the outside of the product and even someone opening the product for repair would have to look carefully to determine where a bolt was made. Still, the two bolts do not meet specifications and part of the job of quality control is to make sure products meet specifications. He should certainly not keep quiet. His job is to report quality problems when he finds them. He has found a problem.
Cosmetic flaws are a common quality problem.
They are, I believe, seldom resolved by trying to slip the product past a customer. If so, the quality problem is not merely cosmetic. The only alternative, then, is to replace the bolts now, whatever the delay and whatever the expense to Clarke, or to try to get out of the contract. While I doubt any quality control engineer would seriously consider passing the bolts on his own authority, the plant manager might. Timely delivery is usually important when one company considers buying from another.