I made some additional tests. It seems that such objects like runways, landing pads, hangars, and so on, are visible through the ground due to shadows from these objects. I placed the VAB mesh in the mountains, chose the texture Runway2.dds for this mesh and tried three cases:
View attachment 36349
Results:
View attachment 36350
In the first case the mesh with its texture isn't shining through the ground. So, maybe we should just make a flat mesh (I just haven't learned how to do it yet) with the texture of a runway, if we want the runway (and other objects) not to be visible through the terrain? It just sounds so simple

Or not, and this idea won't work?