A valid reason is just not required for the the engineer to specify metal boxes. If I designed it specifying metal boxes and the EC used plastic boxes, I would not accept any type of credit. I would require the EC to comply with the contract documents.Then you don't want to be in the electrical business do you? The OP isn't a contractor but instead an inspector, so the credit issue doesn't apply to him, but having been involved in many, many projects that have been value engineered and/or have specs that aren't compatible with each other, I can think of a dozen valid arguments right off the top of my head on how I would fight a request for a credit for plastic boxes. It very much depends on the situation. There is just no valid reason to require metal boxes with NM cable. If you are going cheap, then go cheap. Engineers are subject to the same problems the rest of us are. They have boilerplate specs, and they don't get paid enough to go through every item of a spec and make sure that it is perfect, so they miss things like this when a job is outside their normal spec wheel house. As an estimator it should be picked up an and at least clarified in the bid, but sometimes the estimator is under the same constraint.
It is extremely unlikely that I would give back a credit for this on a job I estimated and ran. I have spent years honing the skill of identifying counter arguments. One of the best ones is that you always pay attention to the little things you do because you know they must be done even though the plans don't indicate it properly. Like when they show hash marks on a plan and the number of wires is wrong. You don't pull the wrong number of wires, you just do it. That becomes very handy when you explain that you didn't install (or price) metal boxes when plastic was in line with the intent of the drawings, you just did it.