Seems like an odd conceit for Apple to make, particularly since they've been pushing the accuracy of their 3D maps, and since you can easily rotate the map in 3D to get a full view of everything. My guess is that their algorithm to calculate the height of buildings from satellite imagery messed up.
No, because if you view in 3D view using satellite mode, the buildings all look the correct height, indicating that the algorithm can work correctly. It seems to be specific to the 3D non-satellite (what they call "map") view. Which suggests it might be an intentional design decision to try to reduce masking. Very weird.
