It's pretty much not a factor.
Here's an example:
2700 f/s M855
200 meter zero
2.5" LOS over bore (iron sight height):
50 meter impact: .63" high
100 meter impact: 1.96" high
3" LOS over bore (optic too high to cowitness):
50 meter impact: .25" high
100 meter impact: 1.71" high
As you can see, the closer zero magnifies the effect of the sight height difference, and even then, the difference is negligible.
For reference, with AR pattern rifles, top of rail is right around 1.2 inches above bore.
A rail-mounted front sight will be between 1.2 and 1.5 inches above the rail (depends on how far in/out it needs to be to achieve zero).
Ballistic calculators use the distance between the line of sight and the muzzle (this will be important in a second).
The sight offset is therefore 2.4-2.7 inches over bore. I usually use 2.5 inches for iron sights.
A standard height 1.5 inch optic base generally gives a 2.6-2.8 inch height, depending on tube thickness, once zeroed.
Lower 1/3 cowitness sights are usually 1.6 inches above rail (to center of glass), for 2.8, but it's a little less at the muzzle.
A NVG height non-cowitnessing sight will be about 1.9 over rail, for a 3.1 inch offset, closer to 3 at muzzle.
For simplicity, I use the following:
Irons and absolute cowitness optics: 2.5"
Lower 1/3, and optics in standard 1.5" mounts: 2.7"
NVG Height/High Mounts: 3.0"
And really, if you're using a 100 yard/meter or further zeroing concept you can just use 2.7 across the board and be just fine out to 1,000 meters without having data confliction.
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