The thickness of each stair tread does not affect the total rise whatsoever. When the stair stringer is laid out, the thickness of the stair tread is taken off the bottom of the stair stringer and added on at the top when you install the stringer, so it cancels itself out.
When you put on the stair tread, the rise remains the same, since you add the thickness of the stair tread on the top of the riser and subtract the thickness on the bottom of the same riser. These two also cancel each other out.
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