Yes. If you think about it, the sights have to be adjusted to raise the strike of the bullet 2.5 inches (roughly) at 50 yards to account for the distance between the sights and the rifle bore. So 25 yards is halfway to 50 yards, so you might see 1.25ish low.
Here is what the trajectory charts at using the Hornady Ballistic Calculator (xm193 is the military 5.56 55gr cartridge):
The red circle shows the bullet 2.5 inches low (because the barrel is below the sights) at 25 yards;
The blue circle shows the NEAR ZERO at 50 yards;
The green circle shows the FAR ZERO between 200 and 225 yards.
Your Troy sight's apertures should be same plane, which means the center of each aperture is at the same point above the bore. So it shouldn't make any difference which aperture you use, small or large.
Attachment 63044
Hope this helps.
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