If you zero at other than 25M, will that throw off the elevation wheel marks?
No. If you read the IBZ procedure, you see that it recalibrates the lowest setting of the wheel for a 200m zero using the long range (small peep) aperture. This allows for a 200m setting two clicks down from the 300m setting (four clicks down with a detachable carry handle). The 300m setting and all others are left to work at their indicated distances. It really is a win-win procedure that gives you settings for 200m, 300m, 400m, 500m, 600m, 700m, and 800m with an A2 fixed carry handle (only up to 600m with a detachable carry handle.
From IBZ Procedure:
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5. The lowest sight setting, however, on these sights is 300 meters so the sight needs to be modified to preserve the markings on the sight (despite the fact that no one ever sets a range on these in the real world other than a USMC range). The sight needs to be set to bottom out at 8/3 -2 clicks. This will be the new 200-meter setting."
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9. If you have to shoot targets you KNOW are 300 meters away or more, just click to the right number on the sight."
Doesn't it also depend on ammo used. Mil rifles use M855, what are you going to use?
No matter where you zero at, the M16A2 sight itself(and it's civilian offspring) is calibrated for M855 62gr ball. However, the ballistics between M193 55gr. and M855 62gr. are so close that it's not going to matter much at all. The accepted tolerance of accuracy for the ammo is more than the difference (ie. the ammo itself might not shoot to better than 2-3 MOA from a rest with perfect wind conditions).