Here we have a case of an airport anomaly not caused by high-resolution terrain mesh, but by erroneous flatten elevation parameter in default water polygons.  Using georeferenced aerial images, the runway was slightly misplaced, which has been corrected, as well as adjustments to the airport property polygon, runways markings, surrounding terrain, some landclass, and the offending water polygons were replaced, bringing the airport environment to a more accurate depiction of its real-life counterpart.

Degali Airport (ENDI)