I think it's a mixture of both. When we create a building pad we force the terrain to adapt to a building either by suppressing the land or elevating it. From there it is quite easy to build up and create your building. At the same time, I think it would be best to keep the changes of the terrain to a minimum. For one, it would decrease disturbance of the site. I also think it would be more expensive to alter the terrain too much, and depending on when the client would like their project to be complete, the alteration of the terrain might add too much time.

The advantages of stacking the levels of a multi-story building is that it's a quick and easy option. All you have to do is copy and paste the walls (aligned by level). From there you can make small changes to the layout as needed. However, when the lower level from what you plan on constructing on the upper level are radically different then it wouldn't make any sense to stack the levels. If a building weren't vertically stacked makes me think of a treehouse of sorts where the main buildings are separate and at different specified heights. It also makes me think of buildings that look like they are a jenga puzzle with random pieces sticking out of the main frame.

The stairs follow specific proportions with a set relationship between the tread length and riser height so that it is a comfortable and natural tread up or down the stairs. The set relationship also exists for safety reasons. Sometimes stairs can be too steep (high riser height) which can be difficult to up but also dangerous to go down. The tread length is also very important because if the tread length is too short than people can trip or stub their foot. The relationship is set by what feels more natural and hopefully less likely to cause accidents.