Ok. So both the front and rear sight cannot be closer together. As in, both mounted on the pic rail on top of the receiver
What will happen is the rear sight will be tipped forward 1/3rd of a degree. You will still be able to sight correctly through it to the front sight. Given that you find a rear sight with elevation adjustment, it will still reach the elevation you wish.
Think of the base directing the centered scope down 1/3rd of a degree, as that's what 20 moa is. The parallax points the center of the scope down 20 moa. But, when the rear sight center and the front sight are matched at a given height above the centerline (parallel) of the barrel, there is no 20 moa in the adjustment. It's zero-zero. Bring the rear sight up 2 moa and technically it should about match a 100 yd. zero.
At super extreme ranges, the slightly forward tipped rear sight wil be very slightly low, but that is going to be a very long distance shoot. Mathematically, if you raise the rear sight one inch it will shoot .0006 moa low. In the case where your sight needs to rise .007" per moa based on a 24" sight radius, I doubt you will notice the offset. You would have to be making a shot using 143 moa to see even that miniscule difference.
Now, if both front and rear sight are mounted on one rail, and initial setting is center of bore to center of sight, then yes, the 20 moa would come into play. You would have to lower the rear sight or raise the front sight.
Added:
it doesn't matter the distance between the rear and front sight if they are independently mounted. The slightly forward tip of the rear sight won't affect elevation until extreme distances.