So here's the thing about KML models: altitude modes are important.

When the altitude mode is set to relativeToGround, polygons above elevated terrain are themselves elevated by the height of the underlying terrain in addition to the specified altitude value. Whereas an altitude mode of absolute will place the model at that exact height regardless of the height of the underlying terrain.

Models that span large areas are best placed at an absolute height. Take a look at my Golden Gate Bridge model for an example. If you switch the alt mode to relativeToGround, the southern span of the bridge (where it contacts the land) shoots up by about 10 meters.