So, anyone with a company laptop technically needs to declare that???
No. The definition you are working from is inexact.
"Commercial merchandise" in this context includes goods which are neither yours nor for your use. Thus, a laptop owned by your employer, but assigned to you is not "commercial merchandise." If you are transporting laptops for 3 colleagues, e.g. laptops owned by the employer but assigned to them, then the laptops are "commercial merchandise." But, those same laptops would not be "commercial merchandise" if each colleague brought his own laptop.
In this case, I suspect that there was a miscommunication. When the laptops were originally exported, they should have been registered with CBP. When reimported, there is no duty due, but the registrations should have been produced. Nothing OP could have done better because he was not the person who originally exported them. Had CBP seized them, it would have been for the employer to retrieve them.