I’m disappointed to see that @dan continues to claim that alignment via the lid camera alone is accurate to any reasonable level, and that you can “manually align” with the lid camera alone.
Eventually (perhaps) this capability will be available once the head camera works in concert with the lid camera, but for now, any attempt to “manually align” will lead to poor results.
Even if the lid camera is operating perfectly, there is no way that it can do accurate alignment if the material has any warp at all.
I know I’ve been beating this point to death over the past years, but with @dan’s continued insistence that it is working accurately, I feel the responsibility to repeat this warning.