I will also say that I hate that test, even though it seems to have worked for you this time. There is a lot wrong with it, in particular it takes most lenses (apart from macros) into very close distances where they will quite likely not be at their best. With some zooms, if you calibrate your focus according to that chart, it can be out at normal range and at different focal lengths. Distance should be 50x focal length as a guide.
AF systems are analogue and work to a tolerance, but that test is hyper-critical and can reveal 'problems' that are actually within acceptable tolerance and are as good as it gets, ie perfectly good at normal range. Plus, being so critical, it is very prone to user error.
And as I say, that is a focus test, not a sharpness test. Shoot a distant target where focus errors are minimised and compare lenses that way, but I kind of doubt that Nikon would return any equipment in anything less than 100% order. Also, human nature being what it is, if you think you've got a potential problem, you will find it one way or another