That slight variance is caused by the fisheye effect of the lid camera, and you need to be using Set Focus on each token in order to get multiples aligned correctly.
It works like this…where you click with the Set Focus tool, it takes a measurement at that spot and the view temporarily becomes as if that spot was right under the lid camera. So you would align the design for that token. But then you have to click the Set Focus tool on the next token to align that one. And so on. When you get them all aligned, then you run the job. But each time you click Set Focus somewhere else, the earlier views of the designs that you already aligned are going to change a little. Do not change them again, they are actually placed where they need to be.
To get accurate “physical” results, which is what ultimately counts, you have to be willing to accept that what you see on the screen is going to appear to be slightly off.
It looks like you cut those out though, and if you do that, there is a much easier way to do reverse side engraving that is 100% accurate every time…you just leave them in the backing material and flip them over. Tutorial for that below: