Hieght over bore must be considered.
If you co-witness your iron sights or red dot using the other as the POA, you have not accounted for the difference in the height of each sight's Point of Aim from each other. Unless your dot aligns perfectly with the front sight at the same height above the bore of the barrel, there will be a difference in point of impact at ranges beyond the zero range. Each set should be zeroed independently of the other and then left alone. That way they will be more likely to be in synch at short to moderately not so short ranges. They will never be 100 percent in synch at all ranges because each has a different height above the bore line that needs to be accounted for in the trajectory. At short ranges you may not notice much difference, but the longer the range the greater the variation between each other in hold over required.
It's just physics. The fact that the irons only show in the bottom 1/3 rd confirms this situation. They would have to be in the exact middle of your red dot to be truly co witnessed and have the same hold overs at longer ranges.
Look at all the Trajectory calculators on the web. One of the questions required is the height of the optical center of the sight over the center of the barrel bore.