If you are zeroed at 50, with the elevation knob all the way down, using the 0-200 (large) aperture, regardless of whether the rear blade is over to one side, it is sighted in. The rear blade being over to one side is another issue (canted front sight tower) and would be that way regardless of zero method you use.
OK, If you zeroed at 50, then your still hold right on the target at 100 m, make no changes, but now you will be hitting the target about 2" high. Fine, this is the intentention.
Still, hold right on the bullseye, at 200 m you will be back on bullseye. At 250 you will be about 4" low.
So, you use the large aperture and the elevation knob all the way down for all shooting from 0-250, and just hold directly on the target. KISS!
For 300 m, you flip to the small aperture and dial the elevation knob to 3. 400 m, dial the knob to 4, etc.