Once that was done the crew would install another thin layer of concrete to use to stamp the designs in
I'm sure that would work, but it sounds like a whole lot of extra cost - an entire operation added. When the ICF contractor sets forms in the first place, it seems like he could place pins for the layout of the interior walls and then use those to snap lines off of for the stamper. It might even be worth it to have the carpenter come out and take a look at that time to get agreement. Then, he would be certain to make the walls agree.
If you got to areas in which you felt the uncertainty was just too great, you could go for a pattern that didn't need to line up so perfectly, or even go for a polished concrete instead of a stamp.