Yes, there is worse image quality in the second image, so assuming the test conditions were the same, they appear to have made it worse. So I would suggest recontact their service department and going higher up in the organization so you can get this resolved.
I also suggest that you consider using a different testing method and focus target. What you are using seems to me to be something that will not give reliable, repeatable results.
All companies produce the occasional dud sample of a product. For each one there are many more that work perfectly fine and have satisfied owners. Unfortunately, you got a bad one.
For those who think a $3,000 camera deserves "Premium" support, keep in mind, this is not in the top 1/2 of NIkon's price range. It is a mid range camera priced for significant sales volume. The D3 series and D4 are the premium cameras, and those who use them professionally and belong to NPS get the premium support. Essentially, you bought the equivalent to a very nice Toyota Camry, but you didn't buy a Lexus. I know that sounds harsh, but it is a fact of the market.