Did you remember to enter the measured thickness of the wood into the Unknown Materials slot?
(Side note: The lid camera has a large fish-eye distortion effect because it is a specialty lens designed to take a picture of the entire bed from up close. There is an algorithm in the programming that corrects for that fish-eye effect for placement purposes, but it order to work correctly, we have to enter the thickness of the material, accurately, as measured in inches with a calipers, into the Unknown Materials menu. Without doing that, the variation in placement is magnified. Proofgrade materials have this information coded into the QR code, so you don’t have to do it for Proofgrade materials.)
The fish-eye effect is minimized underneath the lid camera, so if you can place your objects to be aligned there, there will be much less variation.
If you’re talking about the little circles at the top, the current working range is within 1/4" placement. (Can’t see the rulers, so I can’t really tell if that is within the acceptable tolerance.)
If after checking to make sure that the material is not warped (even a mm or two will affect it) and is perfectly flat, try centering the print under the lid camera. If you still see more than 1/4" variation, then the machine might actually have an alignment problem.
Oh, and one last thing to check is to turn the machine off, center the head gently underneath the lid camera, and turn it back on to let it recalibrate. That will often clear up software related alignment issues, which can pop up after the updates get pushed out.
The alignment gets better over time, as they collect metrics for the individual machines and work on the software side, so expect to see it gradually improve.