This question used the phrase on top of to describe an overpass over another road. When one of the answers suggested that "over" would be more appropriate because there is space between the bridge and the road, the questioner disagreed. But I can not think of any situation where I would use on top of when there is no direct contact between surfaces (Northeast US English).
"The bird is on top of the building," means the bird is perched on the building itself.
"The bird is over the building," means the bird is in the air over the building.
Can on top of be used when there is no direct contact between the things below and above? Does this vary regionally?