Can 52.212-4 and 52.246-2 be incorporated in a contract? If so, Does DCMA have a right to perform in process investigations or surveillance. FAR12-102c states, "When a policy in another part of the FAR is inconsistent with a policy in this part, this part 12 shall take precedence for the acquisition of commercial items". Does that invalidate the 52.246-2 clause?
Your question touches on a whole of range of issues concerning commercial contracting partitives. Recently industry has complained that DOD has issued numerous rules and regulations concerning commercial contracts that would seem to violate as you identified the intent of FAR 12.102, FAR 12.000 and FAR 12.101. We are to rely on the contractor's quality control system, FAR 12.208 -- Contract Quality Assurance. And testing is done by the Government at acceptance FAR 12.402 Acceptance. (There are two FAR 52.212-4 clauses, the basic and the alternative; my answer is focused on the basic and not the alternative.) The government depends on the commercial practice of warranties of merchantability and warranty for fitness of a particular purpose FAR 12.404 Warranty. (Merchantability is that the product appears and functions like a reasonable buy would expect it to, the truck has an engine and will turn on, and warranty of fitness is that the seller delivers us a truck that can meet the requirement laid out in the contracts, we need to move a 40 foot container probably a four cylinder pickup truck wouldn't be able to do this.) Further if you look at the FAR Matrix, 52.246-2 is a non-commercial clause.
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Why not then a simple no, the contract shouldn't have FAR 52.212-4 and FAR 52.246-2? Another principle of the FAR is commercial practices. Simply commercial practices of buying a toaster and 50 foot boat can differ considerably. More than likely it is not commercial practices to go to the toaster oven factory and inspect them. But it might be commercial practice in the boating world for the buyer to visit the yard where the boat is laid down. Maybe the end user buys the outboards that will go on the boat separately and provides them to the boat yard along with electronics and other gear. Unfortunately this requires the buying command to know what those commercial practices are and to incorporate specific language into the contract for acceptance FAR 12.402(b).
In conclusion, FAR 52.212-4 and 52.246-2 should not both be in the same contract. Language similar the quality clause could be included but that should be guided by commercial practices and the complexity of the end item. Mixing commercial and non- commercial contract clauses could create enforcement problems for the Government later if the courts had to decide if the clause was enforceable or not.