I think posting the photos helps further the conversation. Here they are mildly sharpened Capture NX2 50-3-4 using a cropped jpg as input (which of course is not as good as it gets).
They look great to me.
And further to clarify that, I also mean that I can't tell from looking at them that your rig is off or not, too many variables in a true wildlife environment like you have shown here. It may well be that your combo rig is within Nikon tolerance, which is what I assume since they did something and sent it back to you.
And it's not that I consider AF Fine tune acceptable. I consider it mandatory But that means you doing it, not Nikon, and using a proper AF fine-tune rig.
After all, you are shooting what I call low tolerance photography. In that game you need every advantage you can get! Sure if folk are not doing what I call low tolerance photography, by all means ignore that feature. But not wildlife guys shooting 600mm behemoths