well you want everything in focus and sharp as possible when looking at it at 1:1
can you post a small crop of a source photo at 1:1?
maybe also do a test to see how sharp you can get a photo while on tripod and using manual focus and live view. just to see how sharp you can get it at 1:1. that might tell you if you are getting a slightly off autofocus point.
but testing with a different canon lens is a good idea too.
as long as you get it reasonably sharp it should be ok.
now looking at your issue, i think i have seen similar things on some of my models, but it hasn’t happened in the main area, but off to the side that wasn’t covered by a lot of photos.
though i have to stay not all of my photos I’ve been putting in are 100% sharp at 1:1 and its still be doing a pretty good job of it.
I’m using D810 and D800e for it. and I still feel it could be sharper at 1:1
I hope you get it figured out. it should really be one of the best cameras out there for doing this kind of work.
chris