I also used to have this problem. But in some DE patch, they made it so that the selection box represents the correct tile. That has help in detecting holes in walls a bit more easily. Just double click a house to select them all and see the boundaries.
Currently, the farm is the only building that adjusts correctly with elevation. (That is because it changes the terrain itself.) I have seen some games skew the building graphics when built on slanted terrain. This would improve the legibility of where the buildings are but skewed buildings look a bit odd. Another method could be to create different building graphics for each different tile elevation configuration (with for example stilts, foundation fillings, dugouts etc.). But I guess this would massively increase the number of sprites needed for each building graphic.