Lilith is more like 7km under the Geofront, the image you posted in the Geofront/Moon stuff thread is wrong :
The geofront is only the "lens" just under Tokyo-3, just under there's the giant 13km wide sphere(chalice/screw in Rebuild) that is the Black Moon, with Lilith at the center of it.
The 15km deep impact calculations of Sahaquiel crashing on Earth assume that what's below the Geofront is just regular ground and rock, not the Black Moon which is extremely resistant(only an handful of NERV members know that they are actually inside a nigh-indestructible crashed alien spaceship)
Had Sahaquiel won and crashed on Earth, he would had probably only blasted through enough of the Black Moon to reach Lilith, since he wants to fuse with her, not vaporize her.