It's actually a (minor*) bug - 6Y3 was exported with an elevation of 0 (ft AMSL), whereas 3MI2 was exported with correct elevation (616 ft AMSL). When Runways follow terrain is active, the airport elevation is ignored by X-Plane, and the airport is rendered on top of the underlying mesh. If the option is disabled, or the airport definition specifies "always flatten", X-Plane ignores the mesh and creates a plateau using the specified airport elevation and the airport boundary - in this case, at 0 ft. Hence the funny "Moses" effect.
*Doesn't make sense to use the scenery for 6Y3 without runways follow terrain - the runway is significantly sloped, and the terrain mesh shipped with the scenery doesn't cause any problems (steps, holes, ... whatever you may encounter out there in the "wild").