A 20 MOA base should not cause any problems getting a rifle zeroed at 100 yards.
If the scope has 50MOA elevation available and it zeroes right in the center of that range (with a flat base) you would end up with 25MOA up and 25MOA down. When you put a 20MOA base under it you should, in theory, be getting an addition 20MOA of useful elevation back. That would give you 45MOA of elevation which should be enough to get a 175gr SMK to 1K yards unless you're shooting a 16" barrel.